Energy-dispersive X-ray analysis on thin sections and unimpregnated soil material.

A combination of scanning electron microscopy (SEM) and energy-dispersive X-ray analysis (EDXRA) was used in the study of soil materials. The investigation in situ of components in thin sections was used to estimate chemical elements with atomic numbers 11 upwards, from sodium on. EDXRA could detect chemical elements up to magnifications of X 10 000. The composition of amorphous and micro-crystalline materials cannot be estimated in thin sections by light microscopy but by this technique was clearly displayed. Composition of loose soil material can also be investigated. The material that could be studied by SEM-EDXRA did not need high polishing of the thin section, and the plastic used for impregnation of the soil material was not affected by the investigation.Identification of chemical elements in situ, high resolution of the topographic image and relatively short testing times for the elements make this combination of techniques useful for soil research. (Abstract retrieved from CAB Abstracts by CABI’s permission

Chemical element detection in thin sections of soils with the Laser Microprobe Mass Analyzer (LAMMA 500).

Components from thin sections of soils developed on weathered granite were analysed with the Laser Microprobe Mass Analyzer. Fragments of thin sections were mounted on sandwich grids, and perforated with the laser from the edges inwards (laser milling), using the laser light at grazing incidence. Laser-induced mass spectra of secondary titanium compounds and other constituents in the weathered granite were obtained in this manner. Positive and negative laser desorption mass spectra were recorded with such a speed and accuracy that in spite of the relatively large volume of analysed materials, minute changes in composition could be detected over very short distances. This allowed total chemical element analysis of spots in which titanium compounds concentrated during weathering, giving information on changes in purity of amorphous and semi-crystalline materials at such sites. Characteristic analysis possibilities of the Ion Microprobe Mass Analyzer (IMMA), Laser Microspectral Analyzer (LMA) and Laser Microprobe Mass Analyzer (LAMMA 500) are compared. (Abstract retrieved from CAB Abstracts by CABI’s permission

Wavelength and energy-dispersive X-ray microanalysis with EMA and SEM-EDXRA on thin sections of soils.

Organic matter, minerals and iron-manganese nodules were studied in thin sections of soils with an electron microprobe analyzer (EMA) and a combination of a scanning electron microscope (SEM) and an energy-dispersive X-ray analyzer (EDXRA). Both instruments were used to estimate the presence and nature of chemical elements in two selected areas, one containing a combination of organic and mineral material and another inside an iron-manganese nodule. The detection of organic matter proved problematic. Of the light elements, N could not be detected with EMA and O was detected but was not specific to organic matter. EMA could not be used for C because of the C coating of the thin section. SEM-EDXRA only detected heavier elements. EMA produced somewhat better X-ray images of heavier elements, especially from an iron-manganese nodule. However, with organic material, SEM-EDXRA X-ray images were similar to or slightly better than EMA. An advantage of SEM-EDXRA over EMA is that the soil material can be analysed at various magnifications with a much higher limit, and point analysis can be made of loose material. For soil material, SEM-EDXRA was better as a routine instrument which solved most problems. EMA can be used as a complementary instrument. Other microanalytical techniques such as the ion microprobe mass analyzer (IMMA) were necessary to analyse light elements in organic material of soils. (Abstract retrieved from CAB Abstracts by CABI’s permission

Light and heavy element detection in thin sections of soils with the ion microprobe mass analyzer (IMMA).

Previous research with the scanning electron microscope (SEM)-energy dispersive X-ray analyzer (EDXRA) and the electron microprobe analyzer (EMA), showed that the detection of light elements in thin sections of soils was problematic or even impossible. Consequently initial experiments were performed with the ion microprobe mass analyzer (IMMA). These preliminary investigations were carried out on a piece of root material in soil (containing both light and heavy elements) which has a 'clayey' appearance and is known as a clayified root (Parfenova et al., 1964). The presence of heavier elements in this sample was investigated by SEM-EDXRA prior to IMMA analysis. The results with the ion microprobe mass analyzer showed that all chemical elements could be analyzed in the plant fragment. Also much higher elemental detection sensitivities were found with IMMA as compared to SEM-EDXRA and EMA. This even allowed ion imaging of trace elements. High-quality ion images of both light and heavy elements could be obtained in much shorter exposure times than with SEM-EDXRA and EMA techniques. Furthermore by analysis of fragmentation ('fingerprint') spectra additional information was obtained with respect to the chemical binding of the analyzed elements. Due to these preliminary results IMMA offers full possibilities for microchemical analysis in situ of all important elements in soil specimens. This technique considerably increases possibilities in soil micromorphology. (Abstract retrieved from CAB Abstracts by CABI’s permission

Carbon monoxide conversion by thermophilic sulfate-reducing bacteria in pure culture and in co-culture with Carboxydothermus hydrogenoformans

Biological sulfate (SO4) reduction with carbon monoxide (CO) as electron donor was investigated. Four thermophilic SO4-reducing bacteria, Desulfotomaculum thermoacetoxidans (DSM 5813), Thermodesulfovibrio yellowstonii (ATCC 51303), Desulfotomaculum kuznetsovii (DSM 6115; VKM B-1805), and Desulfotomaculum thermobenzoicum subsp. thermosyntrophicum (DSM 14055), were studied in pure culture and in co-culture with the thermophilic carboxydotrophic bacterium Carboxydothermus hydrogenoformans (DSM 6008). D. thermoacetoxidans and T. yellowstonii were extremely sensitive to CO: their growth on pyruvate was completely inhibited at CO concentrations above 2% in the gas phase. D. kuznetsovii and D. thermobenzoicum subsp. thermosyntrophicum were less sensitive to CO. In pure culture, D. kuznetsovii and D. thermobenzoicum subsp. thermosyntrophicum were able to grow on CO as the only electron donor and, in particular in the presence of hydrogen/carbon dioxide, at CO concentrations as high as 50-70%. The latter SO4 reducers coupled CO oxidation to SO4 reduction, but a large part of the CO was converted to acetate. In co-culture with C. hydrogenoformans, D. kuznetsovii and D. thermobenzoicum subsp. thermosyntrophicum could even grow with 100% CO (P CO=120 kPa)

Proteome and Membrane Fatty Acid Analyses on Oligotropha carboxidovorans OM5 Grown under Chemolithoautotrophic and Heterotrophic Conditions

Oligotropha carboxidovorans OM5 T. (DSM 1227, ATCC 49405) is a chemolithoautotrophic bacterium able to utilize CO and H2 to derive energy for fixation of CO2. Thus, it is capable of growth using syngas, which is a mixture of varying amounts of CO and H2 generated by organic waste gasification. O. carboxidovorans is capable also of heterotrophic growth in standard bacteriologic media. Here we characterize how the O. carboxidovorans proteome adapts to different lifestyles of chemolithoautotrophy and heterotrophy. Fatty acid methyl ester (FAME) analysis of O. carboxidovorans grown with acetate or with syngas showed that the bacterium changes membrane fatty acid composition. Quantitative shotgun proteomic analysis of O. carboxidovorans grown in the presence of acetate and syngas showed production of proteins encoded on the megaplasmid for assimilating CO and H2 as well as proteins encoded on the chromosome that might have contributed to fatty acid and acetate metabolism. We found that adaptation to chemolithoautotrophic growth involved adaptations in cell envelope, oxidative homeostasis, and metabolic pathways such as glyoxylate shunt and amino acid/cofactor biosynthetic enzymes

Isolation and characterization of a new CO-utilizing strain, Thermoanaerobacter thermohydrosulfuricus subsp. carboxydovorans, isolated from a geothermal spring in Turkey

A novel anaerobic, thermophilic, Gram-positive, spore-forming, and sugar-fermenting bacterium (strain TLO) was isolated from a geothermal spring in Ayaş, Turkey. The cells were straight to curved rods, 0.4–0.6 μm in diameter and 3.5–10 μm in length. Spores were terminal and round. The temperature range for growth was 40–80°C, with an optimum at 70°C. The pH optimum was between 6.3 and 6.8. Strain TLO has the capability to ferment a wide variety of mono-, di-, and polysaccharides and proteinaceous substrates, producing mainly lactate, next to acetate, ethanol, alanine, H2, and CO2. Remarkably, the bacterium was able to grow in an atmosphere of up to 25% of CO as sole electron donor. CO oxidation was coupled to H2 and CO2 formation. The G + C content of the genomic DNA was 35.1 mol%. Based on 16S rRNA gene sequence analysis and the DNA–DNA hybridization data, this bacterium is most closely related to Thermoanaerobacter thermohydrosulfuricus and Thermoanaerobacter siderophilus (99% similarity for both). However, strain TLO differs from Thermoanaerobacter thermohydrosulfuricus in important aspects, such as CO-utilization and lipid composition. These differences led us to propose that strain TLO represents a subspecies of Thermoanaerobacter thermohydrosulfuricus, and we therefore name it Thermoanaerobacter thermohydrosulfuricus subsp. carboxydovorans

Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium

Clostridium autoethanogenum is an acetogenic bacterium capable of producing high value commodity chemicals and biofuels from the C1 gases present in synthesis gas. This common industrial waste gas can act as the sole energy and carbon source for the bacterium that converts the low value gaseous components into cellular building blocks and industrially relevant products via the action of the reductive acetyl-CoA (Wood-Ljungdahl) pathway. Current research efforts are focused on the enhancement and extension of product formation in this organism via synthetic biology approaches. However, crucial to metabolic modelling and directed pathway engineering is a reliable and comprehensively annotated genome sequence