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  • 1
    Electronic Resource
    Electronic Resource
    Oxford, UK; Malden, USA : Blackwell Science Ltd
    ISSN: 1365-2389
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Analysis of soil lipids may contribute to an improved understanding of atmosphere to soil carbon fluxes, soil organic matter source differentiation and pollutant accumulation. Soil lipids, mostly originating from plants and microorganisms, have traditionally been analysed by non-automated extraction and separation methods, which produce several lipid fractions, operationally defined by polarity. Here we present a combination of fast, automated and reproducible techniques, adopted from organic geochemical studies, for preparative separation of individual soil lipid fractions with increasing polarity. These techniques involve commercially available instruments, including accelerated solvent extraction and a two-step automated medium-pressure liquid chromatography procedure. The method yields eight lipid fractions consisting of five fractions fully amenable to gas chromatography/mass spectrometry (GC/MS) (aliphatic hydrocarbons, aromatic hydrocarbons, ketones, alcohols, carboxylic acids), and three fractions of highly polar or high molecular weight compounds (bases, very long-chain wax esters (C40+), high polarity compounds) that were not measurable with GC/MS under standard conditions. We tested the method on five agricultural soils. Results show that (i) mass recoveries for the individual fractions are reproducible, (ii) within individual fractions compound distribution patterns are reproducible, as demonstrated for alkanes and carboxylic acids, and (iii) individual fractions represent distinct and clean compound classes, free of interfering substances detectable by GC/MS. Thus, automated separation can be a fast, effective and reproducible procedure for fractionation of complex mixtures of soil lipids into clean compound classes, directly suitable for a variety of molecular (e.g. GC/MS) and isotopic characterizations (e.g. gas chromatography coupled with isotope ratio monitoring mass spectrometry or accelerator mass spectrometry).
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  • 2
    ISSN: 1365-2389
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Burning vegetation produces partly charred plant material which subsequently could contribute to the highly refractory proportion of soil organic matter. The presence of charred organic carbon (COC) was investigated in 17 horizons originating from nine soils from Germany and the Netherlands using a suite of complementary methods (high-energy ultraviolet photo-oxidation, scanning electron microscopy, solid-state 13C nuclear magnetic resonance, lignin analysis by CuO oxidation). Charred organic carbon could not be detected in the A horizons of an Alisol and a Gleysol, but it contributed up to 45% of the organic carbon and up to about 8 g kg–1 of the soil in a range of grey to black soils (Cambisol, Luvisol, Phaeozem, Chernozem and Greyzem). All these soils have chernozemic soil properties (dark colour, A–C profile, high base saturation, bioturbation). A 10-km colour sequence of four chernozemic soils, which were very similar in chemical and physical properties, showed a strong relation between colour and the content of COC. This suggests that the COC affects mainly soil colour in the sequence studied. Finely divided COC seems to be a major constituent of many chernozemic soils in Germany. These results suggest that besides climate, vegetation and bioturbation, fire has played an important role in the pedogenesis of chernozemic soils.
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  • 3
    ISSN: 1365-2389
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Soils and sediments contain only small amounts of organic matter, and large concentrations of paramagnetic metals can give poor solid-state nuclear magnetic resonance (NMR) spectra of organic matter. Pretreatment of samples with hydrofluoric acid (HF) dissolves significant proportions of the mineral matrix and extracts paramagnetic elements. We investigated the effects of 10% HF treatment on the stable isotope content of carbon (C) and nitrogen (N) of organic matter from soils, composts and shales. Additionally we inferred molecular and isotopic characteristics of lost materials from calculations of isotope mass balances. Treatment with HF enriched C and N in mineral samples substantially (factors 2.5–42.4), except for Podzol B horizons (1.1–1.7) and organic material (1.0–1.3). After treatment most of the C (59.7–91.7%) and N (53.7–86.6%) was recovered, although changing C/N ratios often indicated a preferential loss of N-rich material. Isotope ratios of C and N in the remaining material became more negative when net alterations exceeded 0.3‰. The isotope ratios of the lost material contained more 13C (1–2‰) and 15N (1–4‰) than the initial organic matter. Acid hydrolysis typically removes proteins, amino acids and polysaccharides, all of which are enriched in 13C, and in the case of proteins and amino acids, enriched in 15N as well. We conclude that HF treatment released fresh, soluble, probably microbial, biomass in addition to carbohydrates. Net changes of the bulk chemical composition of organic matter were small for most soils, size fractions and plant material, but not for samples containing little organic matter, or those rich in easily soluble organic matter associated with iron oxides, such as Podzol B horizons.
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  • 4
    ISSN: 1365-2389
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: The organic matter in soils may be stabilized by its interactions with minerals. We have studied such interactions in a Haplic Alisol under forest in which clay and organic matter have migrated from an eluvial A horizon to accumulate in an illuvial B horizon. We have tried to trace the fate of organic matter in these horizons (Ah and Bvt) by determining clay mineralogy, carbon and nitrogen content, hydrolysable amino acids, lignin signature by alkaline CuO oxidation and carbon species by 13C CPMAS NMR of bulk soils and particle-size fractions. In both horizons, most of the organic matter was present in O–alkyl and methylene structures, each contributing one-third to the bulk organic matter. In the Ah horizon the ratios of carbon-to-nitrogen, and yields for lignin and hydrolysable amino acids decreased as the particle-size class decreased, but side-chain oxidation of lignin compounds increased with decreasing particle size. In contrast to previous observations, the proportions of O–alkyl carbon increased as particle size decreased, constituting a major proportion of the organic carbon in the clay-size fractions from both the Ah and Bvt horizons (≥ 38%), while proportions of methylene carbon decreased. Illite was the dominant mineral in the fraction ≤ 6 μm, whereas the mobile fine clay fraction (〈0.2 μm) was rich in smectites – minerals with large surface areas. Our results support the hypothesis that potentially labile organic matter, such as O–alkyl carbon typically present in polysaccharides, may be stabilized against further degradation in organomineral complexes.
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  • 5
    ISSN: 1365-2389
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Soil organic matter can be intimately associated with mineral particles of various sizes. For structural studies, soil organic matter can be isolated in particle size fractions after complete dispersion of the aggregates by ultrasonication. The ultrasonic dispersion energy necessary for complete dispersion was investigated in three A and two B horizons originating from four soils differing in pedogenesis (Gleysol, Phaeozem, Podzol, Alisol), organic C (4.2–34.5 g kg–1) and clay content (24–294 g kg–1). Calorimetric calibration of five probe-type ultrasonifiers revealed that the actual energy output from an instrument can depart widely from its nominal output, and that this discrepancy varies from instrument to instrument. Calorimetric calibration is therefore essential for consistency and comparisons between laboratories. Between 450 and 500 J ml–1 of ultrasonic dispersion energy was enough to disperse completely all samples investigated. The particle size distributions obtained were close to those from standard analysis, except for smaller yields (–20 to –80 g kg–1) of sand size fractions, which suggests that dispersion by ultrasound is more effective. Based on total C, C:N ratio and distribution of dissolved C, no detachment of soil organic matter from primary organomineral complexes and no redistribution between particle size fractions could be detected in the range 30–590 J ml–1 of dispersion energy.
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  • 6
    ISSN: 1365-2389
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Fires in boreal forests frequently convert organic matter in the organic layer to black carbon, but we know little of how changing fire frequency alters the amount, composition and distribution of black carbon and organic matter within soils, or affects podzolization. We compared black carbon and organic matter (organic carbon and nitrogen) in soils of three Siberian Scots pine forests with frequent, moderately frequent and infrequent fires.Black carbon did not significantly contribute to the storage of organic matter, most likely because it is consumed by intense fires. We found 99% of black carbon in the organic layer; maximum stocks were 72 g m−2. Less intense fires consumed only parts of the organic layer and converted some organic matter to black carbon (〉 5 g m−2), whereas more intense fires consumed almost the entire organic layer. In the upper 0.25 m of the mineral soil, black carbon stocks were 0.1 g m−2 in the infrequent fire regime.After fire, organic carbon and nitrogen in the organic layer accumulated with an estimated rate of 14.4 g C m−2 year−1 or 0.241 g N m−2 year−1. Maximum stocks 140 years after fire were 2190 g organic C m−2 and 40 g N m−2, with no differences among fire regimes. With increasing fire frequency, stocks of organic carbon increased from 600 to 1100 g m−2 (0–0.25 m). Stocks of nitrogen in the mineral soil were similar among the regimes (0.04 g m−2). We found that greater intensities of fire reduce amounts of organic matter in the organic layer but that the greater frequencies may slightly increase amounts in the mineral soil.
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  • 7
    ISSN: 1365-2389
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Standard procedure for dispersing natural soils for particle size fractionation can be too aggressive for soil containing coal and other organic particles from coal industries. We have investigated ultrasonic dispersion for the latter in four soils differing in pedogenesis (Phaeozem, Podzol, reclaimed mine soils), carbon content (27.5–138.6 g kg–1), clay content (80–153 g kg–1) and sources of particles (airborne coal dust, combustion residues, lignite particles). As we found previously for natural soils, the ultrasonic energy needed for complete dispersion varies between 450 and 500 J ml–1, but the resulting particle size distributions differ from those obtained by standard textural analysis. This is probably related to the different properties of native soil organic matter and coal and combusted particles. Coal and soot particles may partly resist oxidation with hydrogen peroxide, depending on material and particle size. The diameter of lignite particles, remaining after oxidation, is overestimated in sedimentation analysis by a factor of 1.66. Sand-sized lignite particles can be disrupted by ultrasonication and redistributed to finer particle size fractions. The ultrasonic dispersion and particle size fractionation procedure can be applied to soils containing coal and combusted particles, but caution is needed in interpreting the results if they contain large proportions of coal particles.
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  • 8
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Science Ltd
    Molecular microbiology 45 (2002), S. 0 
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: In recent years, accumulating evidence for glycosylated bacterial proteins has overthrown an almost dogmatic belief that prokaryotes are not able to synthesize glycoproteins. Now it is widely accepted that eubacteria express glycoproteins. Although, at present, detailed information about glycosylation and structure–function relationships is available for only few eubacterial proteins, the variety of different components and structures observed already indicates that the variations in bacterial glycoproteins seem to exceed the rather limited display found in eukaryotes. Numerous virulence factors of bacterial pathogens have been found to be covalently modified with carbohydrate residues, thereby identifying these factors as true glycoproteins. In several bacterial species, gene clusters suggested to represent a general pro-tein glycosylation system have been identified. In other cases, genes encoding highly specific glycosyltransferases have been found to be directly linked with virulence genes. These findings raise interesting questions concerning a potential role of glycosylation in pathogenesis. In this review, we will therefore focus on protein glycosylation in Gram-negative bacterial pathogens.
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  • 9
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: Diffusely adhering Escherichia coli (DAEC) strains have been implicated in epidemiological studies as a cause of diarrhoea in children. However, the molecular interactions of these pathogens with target cells have remained largely obscure. We found that some DAEC strains contain homologues of the locus of enterocyte effacement (LEE) pathogenicity island and secrete EspA, EspB and EspD proteins necessary for the formation of the attaching and effacing (A/E) lesions. To characterize the function of the EspD protein further, we cloned and sequenced the espD genes of two DA-EPEC strains and compared their deduced amino-acid sequences with known EspD sequences. A pattern of two conserved transmembrane regions and one conserved coiled-coil region is predicted in EspD and also in the type III system secreted proteins YopB, PopB, IpaB and SipB of Yersinia, Pseudomonas, Shigella and Salmonella respectively. The EspD protein is inserted into a trypsin-sensitive location in the HeLa cell membrane at sites of bacterial contact, but is not translocated into the cytoplasm. Secretion of EspD increases upon contact with host cells. We propose that the membrane-located EspD protein is part of the translocation apparatus for Esp proteins into the target host cell performing functions similar to YopB in Yersinia.
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