Raman spectroscopy and microspectrophotometry of reactive dyes on cotton fibres: analysis and detection limits.

A collaborative study on Raman spectroscopy and microspectrophotometry (MSP) was carried out by members of the ENFSI (European Network of Forensic Science Institutes) European Fibres Group (EFG) on different dyed cotton fabrics. The detection limits of the two methods were tested on two cotton sets with a dye concentration ranging from 0.5 to 0.005% (w/w). This survey shows that it is possible to detect the presence of dye in fibres with concentrations below that detectable by the traditional methods of light microscopy and microspectrophotometry (MSP). The MSP detection limit for the dyes used in this study was found to be a concentration of 0.5% (w/w). At this concentration, the fibres appear colourless with light microscopy. Raman spectroscopy clearly shows a higher potential to detect concentrations of dyes as low as 0.05% for the yellow dye RY145 and 0.005% for the blue dye RB221. This detection limit was found to depend both on the chemical composition of the dye itself and on the analytical conditions, particularly the laser wavelength. Furthermore, analysis of binary mixtures of dyes showed that while the minor dye was detected at 1.5% (w/w) (30% of the total dye concentration) using microspectrophotometry, it was detected at a level as low as 0.05% (w/w) (10% of the total dye concentration) using Raman spectroscopy. This work also highlights the importance of a flexible Raman instrument equipped with several lasers at different wavelengths for the analysis of dyed fibres. The operator and the set up of the analytical conditions are also of prime importance in order to obtain high quality spectra. Changing the laser wavelength is important to detect different dyes in a mixture.

Modeling biogeochemical dynamics in porous media: Practical considerations of pore scale variability, reaction networks, and microbial population dynamics in a sandy aquifer.

Prediction of the fate and environmental impacts of groundwater contaminants requires the identification of relevant biogeochemical processes and necessitates the macroscopic representation of microbial activity occurring at the microscale. Using a well-studied sandy aquifer environment, we evaluate the importance of pore distribution on organic matter respiration in a porous medium environment by performing spatially explicit simulations of microbial metabolism at the sub-millimeter scale. Model results using an idealized porous medium under non-biofilm forming conditions indicate that while some heterogeneity is observed for flow rates, distributions of microbes and dissolved organic substrates remain relatively homogenous at the grain scale. At the macroscale in the same environment, we assess the impact of a comprehensive reaction network description for a phenolic contaminant plume, and compare the findings to a setting describing organic matter breakdown in a coastal marine sediment. This comparison reveals the importance of reactions recycling reduced metabolites at redox interfaces, leading to a competition for oxidants. When the spatio-temporal dynamics of microbial groups are accounted for, our simulations show the importance of reaction energetics and nutrient limitations such as microbial nitrogen demands.

Natural attenuation of nitrogen loading from septic effluents: Spatial and environmental controls.

We assess the role of septic systems as potential nitrogen (N) sources to coastal open water bodies. To quantify the potential role of septic tanks, we document the distribution pattern and functionality of septic tanks in McIntosh County in Georgia, USA, and examine factors governing the mitigation of septic N loading in coastal groundwater. Employing a field calibrated 2D variable-density reaction-transport model, we focus on the role of setback distance of a leaky septic source from the receiving surface waters, on transport and biogeochemical characteristics of the subsurface environment, and on leachate composition and reactivity. We conclude that the removal of bioavailable nitrogen via denitrification may be increased by increasing the septic system setback distance, in particular in brackish and saline coastal settings where sulfide produced in sulfate reduction can limit N(2) production.

In silico Geobacter sulfurreducens metabolism and its representation in reactive transport models.

Microbial activity governs elemental cycling and the transformation of many anthropogenic substances in aqueous environments. Through the development of a dynamic cell model of the well-characterized, versatile, and abundant Geobacter sulfurreducens, we showed that a kinetic representation of key components of cell metabolism matched microbial growth dynamics observed in chemostat experiments under various environmental conditions and led to results similar to those from a comprehensive flux balance model. Coupling the kinetic cell model to its environment by expressing substrate uptake rates depending on intra- and extracellular substrate concentrations, two-dimensional reactive transport simulations of an aquifer were performed. They illustrated that a proper representation of growth efficiency as a function of substrate availability is a determining factor for the spatial distribution of microbial populations in a porous medium. It was shown that simplified model representations of microbial dynamics in the subsurface that only depended on extracellular conditions could be derived by properly parameterizing emerging properties of the kinetic cell model.

Ecological genomics of marine Roseobacters.

Bacterioplankton of the marine Roseobacter clade have genomes that reflect a dynamic environment and diverse interactions with marine plankton. Comparative genome sequence analysis of three cultured representatives suggests that cellular requirements for nitrogen are largely provided by regenerated ammonium and organic compounds (polyamines, allophanate, and urea), while typical sources of carbon include amino acids, glyoxylate, and aromatic metabolites. An unexpectedly large number of genes are predicted to encode proteins involved in the production, degradation, and efflux of toxins and metabolites. A mechanism likely involved in cell-to-cell DNA or protein transfer was also discovered: vir-related genes encoding a type IV secretion system typical of bacterial pathogens. These suggest a potential for interacting with neighboring cells and impacting the routing of organic matter into the microbial loop. Genes shared among the three roseobacters and also common in nine draft Roseobacter genomes include those for carbon monoxide oxidation, dimethylsulfoniopropionate demethylation, and aromatic compound degradation. Genes shared with other cultured marine bacteria include those for utilizing sodium gradients, transport and metabolism of sulfate, and osmoregulation.