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Burial of organic matter (OM) plays an important role in marine sediments, linking the short-term, biological carbon cycle with the long-term, geological subsurface cycle. It is well established that low-oxygen conditions promote organic carbon burial in marine sediments. However, the mechanism remains enigmatic. Here we report biochemical quality, microbial degradability, OM preservation and accumulation along an oxygen gradient in the Indian Ocean. Our results show that more OM, with biochemically higher quality, accumulates under low oxygen conditions. Nevertheless, microbial degradability does not correlate with the biochemical quality of OM. This decoupling of OM biochemical quality and microbial degradability, or bioavailability, violates the ruling paradigm that higher quality implies higher microbial processing. The inhibition of bacterial OM remineralisation may play an important role in the burial of organic matter in marine sediments and formation of oil source rocks. [ABSTRACT FROM AUTHOR]

Burial of organic matter (OM) plays an important role in marine sediments, linking the short-term, biological carbon cycle with the long-term, geological subsurface cycle. It is well established that low-oxygen conditions promote organic carbon burial in marine sediments. However, the mechanism remains enigmatic. Here we report bio- chemical quality, microbial degradability, OM preservation and accumulation along an oxygen gradient in the Indian Ocean. Our results show that more OM, and of biochemically higher quality, accumulates under low oxygen conditions. Nevertheless, microbial degradability does not correlate with the biochemical quality of OM. This decoupling of OM biochemical quality and microbial degradability, or bioavailability, violates the ruling paradigm that higher quality implies higher microbial processing. The inhibition of bacterial OM remineralisation may play an important role in the burial of organic matter in marine sediments and formation of oil source rocks. [ABSTRACT FROM AUTHOR]

Volcanic ash soils contain very large stocks of soil organic matter (SOM) per unit area. Consequently, they constitute potential sources or sinks for the greenhouse gas carbon dioxide. Whether soils become a net carbon source or sink with climate and/or land-use change depends on the stability of SOM against decomposition, which is influenced by stabilization mechanisms in the soil. To quantify organic carbon stocks and to clarify the importance of chemical and physical soil characteristics for carbon stabilization in volcanic ash soils, we applied selective extraction techniques, performed X-ray diffraction analysis of the clay fraction and estimated pore-size distribution of soils under natural upper montane forest and grassland (páramo) in the Ecuadorian Andes. Our results show that organic carbon stocks under both vegetation types are roughly twice as large as previously reported global averages for volcanic ash soils. SOM stabilization is suggested to be dominantly influenced by the following chemical and physical soil characteristics: (i) direct stabilization of SOM in organo-metallic (Al-humus) complexes, explaining at most 40% of carbon accumulation, (ii) indirect protection of SOM (notably aliphatic compounds) through low soil pH and toxic levels of Al, and probably also (iii) physical protection of SOM caused by a very large micro-porosity. Moreover, in the case of the forest soils, inherent recalcitrance of OM itself was responsible for substantial accumulation in ectorganic horizons. Both vegetation types contributed to soil acidification, thus increasing SOM accumulation. [ABSTRACT FROM AUTHOR]

The processes governing the (im)mobilization of Al, Fe and dissolved organic matter (DOM) in podzols are still subject to debate. In this study we investigated the mechanisms of (im)mobilization of Al, Fe and organic matter in the upper and lower B horizons of two podzols from the Netherlands that are in different stages of development. We equilibrated batches of soil material from each horizon with DOM solutions obtained from the Oh horizon of the corresponding soil profiles. We determined the amount of (im)mobilized Al, Fe and DOM after addition of Al and Fe at pH 4.0 and 4.5 and initial dissolved organic carbon (DOC) concentrations of 10 mg C litre−1 or 30 mg C litre−1, respectively. At the combination of pH and DOC concentrations most realistic for the field situation, organic matter was retained in all horizons, the most being retained in the lower B horizon of the well-developed soil and the least in the upper B horizon of the younger profile. Organic matter solubility seemed to be controlled mainly by precipitation as organo-metal complexes and/or by adsorption on freshly precipitated solid Al- and Fe-phases. In the lower B horizons, at pH 4.5, solubility of Al and Fe appeared to be controlled mainly by the equilibrium with secondary solid Al- and Fe-phases. In the upper B horizons, the solubility of Al was controlled by adsorption processes, while Fe still precipitated as inorganic complexes as well as organic complexes in spite of the prevailing more acidic pH. Combined with a previous study of eluvial horizons from the same profiles, the results confirm the important role of organic matter in the transport of Al and Fe to create illuvial B horizons initially and subsequently deepening and differentiating them into Bh and Bs horizons. [ABSTRACT FROM AUTHOR]

Interactions with dissolved organic matter (DOM) are generally believed to play a crucial role in the translocation of Al and Fe in acid sandy soils. Binding of Al and Fe to DOM affects their mobility in soils by altering sorption equilibria of charged sites on solid soil material, inducing precipitation of organo-metallic complexes and preventing the formation of inorganic Al and Fe phases. The relative importance of the different processes, especially with respect to the translocation of Al, Fe and organic matter in podzols, remains unresolved. We determined the effect of the presence of solid soil material from the eluvial (AhE and AE, respectively) horizons of a Fimic Anthrosol and a Haplic Podzol on the metal-to-organic carbon (M/C) ratio in solution and the formation of dissolved organic Al and Fe complexes. Furthermore, we assessed the resulting influence on the mobilization of Al, Fe and DOM. Even under considerable metal loading, the M/C ratios and ‘free’ metal fractions in solution remained low and relatively constant, due to an apparent buffering by the solid phase and the formation of organo-metal complexes in solution. The M/C ratios remained so low that significant precipitation of organo-metal complexes due to saturation with metals was not found. The apparent buffering by the solid phase can be explained by a strong release of organic matter from solid soil material and adsorption of non-complexed Al and Fe on solid organic matter upon metal addition. Adsorption of organo-metal complexes most likely played only a minor role. The observations confirm the expected mobilization of Al, Fe and DOM in eluvial horizons and seem to indicate that even under fluctuating input of Al, Fe and DOM the soil solution will have a constant composition with respect to M/C ratios and percentage of Al and Fe present in dissolved organo-metal complexes. [ABSTRACT FROM AUTHOR]

The application of lime in a mature Norway spruce (Picea abies [L.] Karst.) forest in southern Germany induced major changes in the activity of soil organisms and root growth. Since this may influence the chemical compostion of the soil organic matter (SOM) of the organic surface layer, its composition and changes due to the treatment were examined in this study. Fine roots of Norway spruce have a relatively low content of extractable lipids, a low alkyl C content (13C CPMAS NMR) and a high ratio of non-cellulosic to cellulosic carbohydrates (NC/CC, carbohydrate determination by MBTH and gas chromatography analyses) as compared to needles. Furthermore, they show high ratios of suberin/cutin compounds (thermally assisted hydrolysis and methylation, (THM)) and high ratios of eicosanic acid/phytadiene I in their lipid extracts (pyrolysis-GC/MS).Liming (4 t ha−1 dolomite) of a Norway spruce organic surface layer decreased the proportion of alkyl C, the alkyl C/O-alkyl C ratio, and the content of extractable lipids. The NC/CC ratio and the abundance of suberin relative to cutin components increased. The contribution of the chlorophyll component phytadiene I decreased in relation to eicosanic acid. These changes are attributed to increased fine root formation in the organic layer after liming. Furthermore, the presence of less degraded lignin (THM, peak ratio of 3,4-dimethoxybenzoic acid, methyl ester/3,4-dimethoxy-benzaldehyde) on the limed plot is explained by the increased input of relatively fresh fine root material. On the other hand, the decrease in the carbon-to-nitrogen ratio may be attributed to the higher microbial activity after liming. [Copyright &y& Elsevier]

Pig (Sus scrofa) feces, separately collected and amended with wheat straw, was composted in a tunnel reactor connected with a cooler. The composting process was monitored for 4 wk and the degradation of organic matter was studied by two chemical extraction methods, 13C cross polarization magic angle spinning (CPMAS) nuclear magnetic resonance (NMR) and pyrolysis gas chromatography–mass spectrometry (GC–MS). Wet‐chemical extraction methods were not adequate to study the degradation of specific organic compounds as the extraction reagents did not give selective separation of hemicellulose, cellulose, proteins, and lignins. A new method was proposed to calculate the contribution of four biomacromolecules (aliphatics, proteins, polysaccharides, and lignin) from the 13C CPMAS NMR spectrum. Pyrolysis GC–MS allowed identification of the composition of the biomacromolecules. The biomacromolecules showed different rates of degradation during composting. High initial degradation rates of aliphatics, hemicellulose, and proteins were observed, where aliphatics were completely degraded and hemicellulose and proteins were partly recalcitrant during the four weeks of composting. The degradation rate of cellulose was much lower and degradation was not completed within the four weeks of composting. Lignin was not degraded during the thermophilic stage of composting but started to degrade slowly during the mesophilic stage. A combination of 13C CPMAS NMR and pyrolysis GC–MS gave good qualitative and semiquantitative assessments of the degradation of biomacromolecules during composting. [ABSTRACT FROM AUTHOR]

To elucidate the mechanism of podzolization in its first stages we studied the fate of the water-soluble organic matter (WSOM) in incipient podzols in sandy soils by comparing the composition of the WSOM from L, F and H horizons with that in the bulk of the Bh horizons and fibres of three profiles. The WSOM appeared to consist significantly of ligno-cellulose and proteins, but these biopolymers were hardly present in the Bh horizons. The material of the fibres, however, greatly resembled the WSOM composition, thereby suggesting that in these soils most of the WSOM is transported through the B horizon and accumulates hardly changed in thin bands where the water stops moving. This implies that in the early steps of podzolization, accumulation of organic matter in the B horizon is not likely to be caused by water-soluble material. [ABSTRACT FROM AUTHOR]

Presents a reply to the comments on the composition of soil organic matter and its water-soluble fraction under young vegetation on drift sand in central Netherlands. Importance of pyrolysis-field ionization mass spectrometry in analyzing aliphatic compound; Use of tetramethylammonium hydroxide as methylation agent in the analyses of aliphatics.

Persistent organic pollutants (POPs) pose a significant global threat to human health and the environment, and require continuous monitoring due to their ability to migrate long distances. Active biomonitoring using cloned mosses is an inexpensive but underexplored method to assess POPs, mainly due to the poor understanding of the loading mechanisms of these pollutants in mosses. In this work, Fontinalis antipyretica (aquatic moss) and Sphagnum palustre (terrestrial moss) were evaluated as potential biomonitors of hexachlorocyclohexanes (HCHs: α-, β-, γ-, δ-HCH), crucial POPs. Moss clones, grown in photobioreactors and subsequently oven-dried, were used. Their lipid composition and distribution were characterized through molecular and histochemical studies. Adsorption experiments were carried out in the aqueous phase using the repeated additions method and in the gas phase using an active air sampling technique based on solid-phase extraction, a pioneering approach in moss research. F. antipyretica exhibited greater lipid content in the walls of most cells and higher adsorption capacity for all HCH isomers in both gaseous and liquid environments. These findings highlight the need for further investigation of POP loading mechanisms in mosses and open the door to explore other species based on their lipid content., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

The heating effect on the soil organic matter (SOM) of a Mediterranean soil was studied in two fractions (macro- and microaggregates) and in two environments (soil under canopy of Quercus coccifera and bare soil between plants). Samples were heated under laboratory conditions at different temperatures (220, 380 and 500°C) to establish their effects on the SOM quality and quantity by comparison with unheated control samples (25°C). The SOM content in the soil under canopy was higher than in the bare one and in the microaggregate fractions than in the macroaggregate ones. Increasing temperatures caused, in general, the decrease of SOM content in both soils as well as in both aggregate classes. The quality of SOM was determined after extraction with 0.1 M NaOH and analysed by pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS). Obtained pyrolysates were characterized by the presence of polyphenols and other aromatic pyrolysis products (lipids, polysaccharides, proteins and lignin derivatives). Some of the products in these control samples, and furthermore the presence of black carbon (BC) markers (e.g. benzene, pyridine and toluene), confirmed the occurrence of past wildfires in the study zone. The composition of the SOM extracted from the soils heated at 220°C, was quite similar to that obtained from unheated soils. The products derived from polysaccharides and lignin, and some coming from polyphenols, were not detected in the pyrolysates of the soil heated at 380 and 500°C., (Copyright © 2011 Elsevier B.V. All rights reserved.)

Pioneer plant species were observed growing on mined areas despite unfavourable conditions such as extreme pH, high salinity and phytotoxic levels of several elements. This study evaluated the contribution of pioneer species to the accumulation of soil organic matter (SOM). We collected 51 samples from 17 non-vegetated, natural and pioneer-vegetated sites in five highly saline mined areas in the Sierra de Cartagena (Spain). The composition of SOM was determined using total C, N and S elemental anlayzer, pyrolysis and solid state (13)C NMR spectroscopy. Results showed that pioneer species like Lygeum spartum had contributed approximately 11 kg SOM kg(-1) soil into the Balsa Rosa sites since 1991; it will take approximately 120 years of continuous growth for this plant to increase the SOM level comparable to natural site. In the Portman Bay area, Sarconia ramosissima and Phragmites australis can contribute SOM equivalent to present day SOM in natural sites in the next 30 years. Low quality SOM (C/N>20) deposited by pioneer plants was dominated by lignin-derived organic compounds such as phenols, guaiacols, syringols and aromatics while polyssacharides and alkyls were the major components in high quality SOM (C/N<20). The addition of SOM to mine wastes is similar to early stages of soil formation and with time, we expect the formation of well-developed Ah horizon on the surface of mine wastes. The presence of P. australis on several sites makes it a very good candidate for successful revegetation of hostile conditions found in many mined sites.

During germinal center (GC) reactions, B-lymphocytes with high-affinity B-cell receptors are selected. Regulation of apoptosis is a key process in selecting such wanted B-cells and in eliminating B-cells with unwanted specificities. In this paper, we show that apoptosis in human GC B-cells involves lysosomal destabilization, which is strictly controlled by caspase-8 activity, but not by caspase-9 activity. Ligation of CD40 provides resistance to lysosomal destabilization. Experimental lysosomal rupture by the lysosomotropic drug O-methyl-l-serine dodecylamide hydrochloride (MSDH) induces apoptosis in GC B-cells, including phosphatidyl serine exposure, mitochondrial inactivation, and DNA fragmentation. These apoptotic features occur in the absence of caspase-3 activity. Follicular dendritic cells (FDCs) protect binding B-lymphocytes from lysosomal destabilization, in both the absence and the presence of MSDH. Our study demonstrates that lysosomal leakage induces apoptosis of GC B-cells in a caspase-3-independent manner and that high-affinity binding to FDCsprevents lysosomal leakage and apoptosis in GC B-cells.

This paper intends to shed light on the interactions between tannin and mineral soil particles. For that purpose, aqueous solution of condensed tannin (CT) (derived from Black pine (Pinus nigra var. maritima)) and commercially available tannic acid (TA) were added to purified quartz (Qtz) sand and quartz sand coated with either goethite (Gt) or ferrihydrite (Fh). After solvent removal by evaporation the samples were extracted by water. The extracts were analysed for organic carbon, total phenolics and CT. The extractability of the two tannins was small and increased in the order Qtz-Fh < Qtz-Gt < Qtz. For all mineral samples, TA was more extractable than CT. Bonding of tannins to the mineral samples and the partial peptisation of the Fe oxide coatings upon the binding resulted in complex tannin release curves. Our results suggest that the inextractability of tannins from natural soils and the absence of tannins in soil leachates might be caused by strong adsorption on soil minerals such as Qtz and Fe (oxy)(hydr)oxides. The results of competition experiments with mixtures of both tannins demonstrate that the CTs, and TA in particular, can release large amounts of Fe (oxides), suggesting that the tannins are excellent metal-mobilising agents. We therefore suggest that the fate of tannins in the mineral soil environment is highly dependent on the abundance of weakly bonded secondary oxides.

Follicular dendritic cells (FDCs) have important functions in the selection of memory B lymphocytes during germinal center reactions (GCR). They present native antigens to potential memory cells, of which only B cells with high affinity B cell receptors (BCR) can bind. These B lymphocytes survive, whereas nonbinding B cells undergo apoptotic cell death. FDCs are present in follicles of any secondary lymphoid organ and belong to the stromal cells of these organs. Ectopic FDC-formation can be found in a number of autoimmune diseases and/or chronic inflammatory situations. This indicates that the development of FDCs is not restricted to secondary lymphoid organs, but that it is rather a matter of local conditions that drives a precursor cell type into FDC-maturation. A precursor of FDCs has presently not been identified, but phenotypic marker studies, in vitro experiments with fibroblast-like cell lines, and recent data on mesenchymal precursor cells from the peripheral blood suggest a close relation to fibroblast-like cells.

The complex architecture of human insulin-like growth factor (IGF) II-leader 1 of 592 nucleotides (nt), with one open reading frame (ORF), and the potential to fold into stable structures makes efficient linear ribosomal scanning difficult to comprehend. Indeed, leader 1-driven reporter expression is low in rabbit reticulocyte lysate. Contrarily, leader 1 is very efficient in cells. Therefore, we tested whether this 5'UTR uses an alternative mechanism for translation initiation in vivo, internal entry or ribosomal shunting. Internal initiation was tested by introducing leader 1 into the intercistronic region of a bicistronic vector. Second cistron expression, driven by leader 1, was lower than by the intercistronic beta-globin 5'UTR, indicating that leader 1 does not contain an internal ribosomal entry site (IRES). Shunting was tested by inserting hairpin (HP) structures, capable of blocking ribosomal scanning, at eight positions in leader 1. After transfection, these mutant 5'UTRs were incapable of directing reporter expression. Less stable HPs at the same positions increased the activity to 50% of wild-type activity, indicating that insertions at these positions are not disastrous for initiation. These data indicate that the translational machinery encounters major parts of leader 1. As scanning seems unlikely, and internal entry and shunting were shown not to occur, we discuss a modified scanning mechanism for architecturally complex 5'UTRs.