Interaction of organic compounds with calcium carbonate—III. Amino acid composition of sorbed layers

Nitrogenous organic compounds in sorbed surface layers and in calcified organic matter associated with calcium carbonate sediment particles consist of 40–50% amino acids, 2% amino sugars and 25% ammonia. In grain size classes > 20 μm these compounds are mainly contained in the calcified protein of carbonate secreting organisms but with smaller grain sizes—and consequently increased specific surface area—they are contained in sorbed layers at the mineral surface. The composition of the sorbed layer is characterized by a predominance of neutral amino acids, a relative enrichment of basic and weakly polar amino acids, and a deficiency of acidic amino acids in comparison with the proteinaceous matter of calcifying organisms. The respective abundances for sorbed and calcified matter are: 505 and 380 Res./ of neutral amino acids, 262 and 450 Res./1000 of acidic amino acids, 92 and 51 Res./l000 of basic amino acids, and 141 and 129 Res./1000 of weakly polar amino acids.The composition of the sorbed layer appears to be the result of sorption of proteinaceous matter from solution since it reflects the free and peptide-bound amino acid composition of seawater. The characteristic amino acid assemblage could also be the result of preferential decomposition of protein and subsequent enrichment of neutral and basic amino acids; however, sorption from solution appears more likely since the total amount of amino acids sorbed to calcium carbonate (0.58 mg m ^?2) corresponds closely to the amount of protein known to cover one m² of aqueous substrate in monolayer arrangement. Sorption from solution is further supported by the low arginine/ornithine ratios in both the sorbed layer and the natural dissolved organic matter. This process might lead to a characteristic amino acid spectrum in fine grained calcareous sediments that reflects the composition of the dissolved organic matter in seawater rather than that of the carbonate secreting proteinaceous matter.     

Dissolved organic matter in pore water of carbonate sediments from Bermuda

Pore water samples from seven nearshore areas in Bermuda were obtained under in situ conditions and analyzed for dissolved organic carbon, dissolved carbohydrates, dissolved free amino acids and dissolved humic substances. The concentration of dissolved organic carbon is higher than in the overlying nearshore waters indicating significant diagenetic remobilization of carbon in these recently deposited carbonate sediments. Dissolved carbohydrates decrease with depth due to microbial utilization.     

Organic matter diagenesis in shallow water carbonate sediments

Muddy carbonate deposits near the Dry Tortugas, Florida, are characterized by high organic carbon remineralization rates. However, approximately half of the total sedimentary organic matter potentially supporting remineralization is occluded in CaCO₃ minerals (intracrystalline). While a portion of nonintracrystalline organic matter appears to cycle rapidly, intracrystalline organic matter has an approximately constant concentration with depth, suggesting that as long as its protective mineral matrix is intact, it is not readily remineralized. Organic matter in excess of intracrystalline organic matter that is preserved may have a variety of mineral associations (e.g., intercrystalline, adsorbed or detrital). In surface sediment, aspartic acid contributed ∼22 mole % and ∼50 mole % to nonintracrystalline and intracrystalline pools, respectively. In deeper sediment (1.6-1.7m), the composition of hydrolyzable amino acids in both pools was similar (aspartic acid ∼40 mole %). Like amino acids, intracrystalline and nonintracrystalline fatty acids have different compositions in surface sediments, but are indistinguishable at depth. These data suggest that preserved organic matter in the nonintracrystalline pool is stabilized by its interactions with CaCO₃. Neutral lipids are present in very low abundances in the intracrystalline pool and are extensively degraded in both the intracrystalline and nonintracrystalline pools, suggesting that mineral interactions do not protect these compounds from degradation. The presence of chlorophyll-a, but absence of phytol, in the intracrystalline lipid pool demonstrates that chloropigments are present only in the nonintracrystalline pool. Sedimentary chloropigments decrease with depth at similar rates in Dry Tortugas sediments as found in alumino-silicate sediments from the Long Island Sound, suggesting that chloropigment degradation is largely unaffected by mineral interactions. Overall, however, inclusion and protection of organic matter by biominerals is a major pathway for organic matter preservation in this low-organic carbon, biomineral-rich regime.     

Origin and composition of organic matter in tidal flat sediments from the German Wadden Sea

Two sediment cores of up to 550 cm length from an intertidal flat of the German Wadden Sea near the island of Spiekeroog were investigated for the quantity and composition of fossil organic matter (OM). The lowermost parts of the cores are dominated by grey mud of a salt marsh facies containing mainly terrestrial OM estimated to account for 60–75% of the total OM, based on δ¹³C values and the ratio of short to long chain n-alkanols. The terrigenous origin of the dominant fraction is indicated, among others, by high proportions of C₂₉ sterols and long chain n-alkanes typical of plant waxes. Coarse shell beds overlying the grey mud at 2–2.5 m depth represent a flooding and erosion event possibly related to heavy storm floods in the Middle Ages. Within the intertidal sand-dominated sediments in the upper parts of the cores total organic carbon (TOC) contents are generally low, ranging from 0.1% to 0.5%, and correlate well with the amount of mud fraction (r² 0.90). At the surface, marine OM has not undergone intense diagenetic alteration and so is the dominant fraction. Eroded peat particles are common throughout most of the sequence and values of the Phragmites peat indicator (PPI) > 5 indicate an origin from reed peat due to a high relative abundance of the n-C₂₄ alkane. Changes in the composition of microbial communities over the depth interval investigated are documented by varying compositions of unsaturated fatty acids with 16 and 18 carbons. Eicosapentaenoic acid (EPA) was detected along the entire cores and indicates the presence of EPA-producing bacterial strains.     

Amino acid and amino sugar yields and compositions as indicators of dissolved organic matter diagenesis

Microbial decomposition experiments were used to characterize changes in the amino acid and amino sugar yields and compositions of natural marine substrates during early diagenesis in seawater. On average, 63% of added carbon and 68% of added nitrogen were removed within the first 30 days of decomposition. In all cases, amino acid utilization accounted for a substantial fraction of the removed C and N. Carbon-normalized amino acid yields decreased to less than 50% of their starting values and most of this change occurred within the first 10 days of decomposition. Increases in the concentrations of amino sugars and decreases in the GlcN:GalN ratio in particulate organic matter (POM) illustrated the significance of microbial production during the decomposition of added substrates. Changes in the mol % composition of amino acids during early diagenesis were substantial but highly variable with substrate. Previous survey data collected from the same region were used in conjunction with the experimental data to investigate the utility of several established amino acid-based indices of organic matter diagenesis. This comparison showed that a combination of these degradation indexes is most effective for describing the diagenetic state of dissolved organic matter (DOM). Carbon-normalized amino acid yields were found to be the most effective indicator for early diagenesis. Relative abundances of amino acids were effective indicators of intermediate stages of diagenesis and the mol % composition of the non-protein amino acid γ-Aba (γ-aminobutyric acid) was an effective indicator of advanced DOM diagenesis.     

Research on the carbon isotopic composition of organic matter from Lake Chenghai and Caohai Lake sediments

The carbon isotopic composition of organic matter from lake sediments has been extensively used to infer variations in productivity. In this paper, based on the study of the contents and δ13C values of organic matter in different types of lakes, it has been found that δ13C values of organic matter have different responses to lake productivity in different lakes. As to the lakes dominated by aqutic macrophytes such as Lake Caohai, organic matter becomes enriched in 13C with increasing productivity. As to the lakes dominated by aquatic algae such as Lake Chenghai, δ13C values of organic matter decrease with increasing productivity, and the degradation of aquatic algae is the main factor leading to the decrease of δ13C values of organic matter with increasing productivity. Therefore, we should be cautious to use the carbon isotopic composition of organic matter to deduce lake productivity.     

Petrographic and geochemical characteristics of organic matter associated with stream sediments in Trail area British Columbia,Canada

Fifty-six samples of stream sediments from 12 creeks in the vicinity of Trail, British Columbia, Canada were examined to determine their origin, characterize their organic matter and their relation to natural/geogenic and anthropogenic sources. The samples were initially screened by Rock-Eval® 6 pyrolysis for their TOC, HI, and OI contents and then examined by both reflected (polarized) and fluorescent light microscopy. It was found that organic matter in stream sediments is mostly from natural/biological sources from local vegetation, such as woody tissue, suberin, spores, and pollen, as well as altered natural/biological input from char formed due to forest fires. Anthropogenic organic matter, mostly coke particles, was also found in the stream sediments. The coke particles have anisotropic properties with medium grained texture formed from medium volatile bituminous coal. The occurrence of coke particles is limited to Ryan Creek located close to an area were some small gold, nickel, and lead smelting operations previously occurred. There is no evidence to indicate that the coke particles found in the creek are emitted from the lead and zinc smelter currently in operation in the area. There are no coal-bearing strata in the area that may have a direct input of coal fragments in any of the creeks.     

Two examples of uranium associated with organic matter

Precambrian carbonaceous material from Cluff, Saskatchewan (Canada), and samples of Late Carboniferous material from Arlit (250 km NNW of Agadès, Niger), were studied by high resolution transmission electron microscopy and energy dispersive X-ray analysis. The Cluff sample is very rich in uranium, whereas those from Arlit are poorer. An intact organo-uranium complex is the major component of the Cluff sample, the carbon and oxygen content of which are high. Uraniferous fragments show very small molecular orientation, whereas those that are uranium-free present a statistical long range preferred orientation. The carbonaceous material of Arlit is entirely free of uranium and behaves as any other humic poorly evolved material; it acquires a small molecular orientation on heat treatment. Uranium was found associated with titaniferous illite in the form of poorly crystallized UTi₂O₆ (Brannerite). The formation of brannerite is attributed to a topotactic transformation of clay particles containing adsorbed organic matter. Clay yields TiO₂; organic matter is the source of UO₂. Destruction of clay leads to release of organic matter, free of uranium, which undergoes diagenesis.     

Forms and bioavailability of phosphorus associated with natural organic matter

Natural organic matter （NOM） is an important ingredient in soil which can improve physical, chemical, and biological properties of soils and nutrient supplies. In this study, we investigated the spectral features and potential availability of phosphorus （P） in the IHSS Elliott Soil humic acid standard （EHa）, Elliott soil fulvic acid standard Ⅱ （EFa）, Waskish peat humic acid reference （WHa）, and Waskish peat fulvic acid reference （WFa） by fluorescence spectroscopy, FT-IR, solution 31P NMR, 3-phytase incubation and UV irradiation. We observed more similar spectral features between EHa and EFa as well as between WHa and WFa than between the two humic acids or two fulvic acids themselves. Phosphorus in WHa and WFa was mainly present in the orthophosphate form. However, only about 5% was water soluble. After treatment by both UV irradiation and enzymatic hydrolysis, soluble orthophosphate increased to 17% of WHa P, and 10%o of WFa P. Thus, it appears that a large portion of P in Waskish peat humic substances was not labile for plant uptake. On the other hand, both orthophosphate and organic phosphate were present in EHa and EFa. Treatment by both UV irradiation and enzymatic hydrolysis increased soluble orthophosphate to 67% of EHa P and 52% of EFa P, indicating that more P in Elliott soil humic substances was potentially bioavailable. Our results demonstrated that source （soil vs. peat） was a more important factor than organic matter fraction （humic acid vs. fulvic acid） with respect to the forms and lability of P in these humic substances.     

Spectral fingerprinting of soil organic matter composition

Large scale environmental monitoring schemes would benefit from accurate information on the composition of soil organic matter (SOM), but so far routine procedures for describing SOM composition remain a chimera. Here, we present the initial assessment of a two step strategy for expeditious determination of SOM composition that involves: (i) building infrared fingerprints from near and mid infrared spectroscopies, two rapid and cheap yet reliable technologies; and (ii) calibrating such infrared fingerprints with multivariate chemometrics from a molecular mixing model based on the more expensive and time consuming ¹³C nuclear magnetic resonance technique, which discriminates five biochemical components: carbohydrate, protein, lignin, lipid and black carbon. We show fair to excellent predictive ability of the calibrated infrared fingerprints for four out of these five biochemical components, with cross-validated ratios of performance to inter-quartile distance from 3.2 to 8.3, on a small set of 23 soil samples with a wide range of organic carbon content (12–500 g/kg). Multivariate calibration models were highly selective (<2% of infrared data were used for all models). However, the specificity to one particular biochemical component of the infrared wavebands automatically selected by each model was relatively low, except for lipid. Achieving direct predictions of SOM composition on unknown soil samples with infrared spectroscopy alone will require further independent validation and a larger number of samples. Overall, the implementation of our strategy at a broader scale, based on available ¹³C nuclear magnetic resonance soil libraries, could provide a cost effective solution for the routine assessment of SOM composition.     

Rapid sampling of organic matter in flooded soils and sediments

Estuaries and Coasts - A coring system using a compressed air supply and a sediment shaking procedure using a soil dispersant are described which greatly simplify and shorten the task of...     

The distribution and source of organic matter in reservoir sediments

The bottom sediments of two reservoirs, one with significant river sediment input and one without, were analyzed for organic matter content. Lake Texoma sediments average 1.0% organic carbon, of which 0.26% organic carbon is deposited by the river sediments of the Red and Washita River deltas. In Fort Gibson reservoir, where there is minimal river sediment input, the organic carbon averages 1.2% and is deposited with a strong correlation to water depth (+0.9). There is a significant difference between the C/N ratio of Lake Texoma sediments (11.5) and Fort Gibson sediments (9.6). The higher C/N ratio is suggested to be a result of the larger input of terrestrial plant debris (with a high original C/N ratio) by the rivers draining into Lake Texoma and the relatively high resistance of the lignin material in the plant debris to decomposition in the reservoir sediments.     

Abiotic interactions of natural dissolved organic matter and carbonate aquifer rock

Abiotic interactions between natural dissolved organic matter (NDOM) and carbonate aquifer rock may be controlling factors of biogeochemical processes and contaminant fate in carbonate aquifer systems. The importance and effects of these interactions were examined using batch adsorption experiments of soil NDOM and representative carbonate sorbents from the Floridan Aquifer. Adsorption of NDOM carbon to aquifer rocks was well-described using a modified linear model and was mostly reversible. Significant adsorption was observed at higher NDOM concentrations, while the release of indigenous organic matter from the rocks occurred at lower concentrations. Longer interaction periods led to more adsorption, indicating that adsorption equilibrium was not achieved. For relatively pure carbonate rock samples, sorbent surface area was found to be the most important controlling factor of adsorption, whereas the presence of indigenous organic matter and subdominant mineral phases were more important, when they occurred. Preferential adsorption of a high over low molecular weight and humic over fulvic components of NDOM onto carbonate sorbents was detected using liquid size exclusion chromatography and excitation–emission fluorometry, respectively. The presence of NDOM inhibited mineral dissolution, though this inhibition was not proportional to NDOM concentration as surface area and mineralogy of carbonate sorbents played additional roles. Though the NDOM–carbonate rock adsorption mechanism could not be completely determined due to the heterogeneity and complexity of NDOM and sorbent surfaces, it is speculated that both rapid and weak outer-sphere bonding and stronger but slower hydrophobic interaction occur. These results have important implications for groundwater quality and hydrogeologic projects such as aquifer storage and recovery.     

Amino acid biogeo- and stereochemistry in coastal Chilean sediments

The spatial distribution of total hydrolysable amino acids (THAA) and amino acid enantiomers (d- and l-forms) was investigated in sediments underlying two contrasting Chilean upwelling regions: at ∼23 °S off Antofagasta and at ∼36 °S off Concepción. The contribution of amino acids to total organic carbon (%T_AAC: 7-14%) and total nitrogen (%T_AAN: 23-38%) in surface sediments decreased with increasing water depth (from 126 to 1350 m) indicating that organic matter becomes increasingly decomposed in surface sediments at greater water depth. Changes in the ratio between the protein amino acid aspartate and its non-protein degradation product β-alanine confirmed this observation. Furthermore, estimates of THAA mineralization showed that sedimentary amino acid reactivity decreased with both increasing water depth as well as progressive degradation status of the organic matter that was incorporated into the sediment. Reactivity of organic matter in the sediment was also assessed using the Degradation Index (DI) developed by [Dauwe, B., Middelburg, J.J., 1998. Amino acids and hexosamines as indicators of organic matter degradation state in North Sea sediments. Limnol. Oceanogr.43, pp. 782-798.]. Off Concepción, DI was successfully applied to examine the degradation status of sedimentary organic matter at different water depths. However, unexpected results were obtained at the Antofagasta stations as DI increased with sediment depth, suggesting more degraded organic matter at the surface than deeper in the cores. The contribution of peptidoglycan amino acids to THAA was estimated from the concentrations of d-aspartate, d-glutamic acid, d-serine, and d-alanine. Peptidoglycan amino acids accounted for >18% of THAA in all investigated samples. In surface sediments peptidoglycan amino acids accounted for a progressively larger fraction of THAA at increasing water depths (up to >26%). Further, the contribution of peptidoglycan amino acids to THAA increased with increased sediment depth and age (up to 288-year-old) reaching up to 59%. Independent estimates based on d-amino acid concentrations in selected laboratory strains, bacterial counts and the sedimentary concentrations of d-amino acids indicate that a large fraction of the measured d-amino acids (>47 to >97%) originated from cell wall residues rather than from enumerated cells.     

醋酸提取沉积物非碳酸盐来源Mg的实验探究——以西宁盆地中中新世-上新世沉积地层为例

古环境研究中沉积物碳酸盐成分的提取常使用不同浓度的稀醋酸进行。已有的研究表明沉积物的非碳酸盐组分也会对稀醋酸提取组分产生一定影响。查明非碳酸盐组分对稀醋酸溶解Mg的贡献十分重要,可为碳酸盐化学组成定量研究提供必要的约束,也是进一步开展沉积物碳酸盐Mg同位素研究的基础。然而目前对稀醋酸提取非碳酸盐来源Mg的研究尚十分缺乏。本研究选取了5个来自西宁盆地莫家庄剖面中中新世-上新世沉积地层碳酸盐含量各异的沉积物样品开展醋酸溶解非碳酸盐来源Mg的实验研究。实验结果表明,全岩样品的稀醋酸提取组分含有非碳酸盐来源的Ca和Mg,特别是在低碳酸盐含量（< 1%）样品中,非碳酸盐组分的影响十分显著。进一步的多相态连续提取实验表明,交换态和硅酸盐是醋酸提取组分非碳酸盐Mg的主要来源。较高Mg/Ca比值的硅酸盐和交换态端元与低Mg/Ca比值的方解石端元混合,可以解释各样品醋酸提取组分的Mg/Ca比值与Ca、Mg含量成分特征。醋酸提取组分相对较高的Mg/Al比值及其变化表明硅酸盐Mg可能主要来自非晶格位置Mg的溶解（如粘土层间）。醋酸提取组分中的Mg/Al比值显著高于全岩沉积物本身的Mg/Al比值,所以不宜采用固定的全岩沉积物元素比值或者标准物质成分（如上部大陆地壳、标准页岩）来校正在醋酸提取组分中硅酸盐溶解对Mg的贡献。

     

Sulfate reduction and the nature of organic matter in estuarine sediments

The reduction of sulfate by sulfate reducing bacteria in the anoxic zone is an extremely important process during early diagenesis of marine sediments. Our data from Great Bay, NH reinforce the proposal that the rate of sulfate reduction is directly proportional to the reactivity of the organic matter or the amount of readily metabolizable organic matter present in the sediment and, hence, the source of the organic material in the anoxic zone. It appears that organic matter rich in marine organic remains is more easily degraded in the anoxic zone and that sulfate reduction rates can vary considerably in an estuarine system where many types of organic material may be deposited.     

Organic geochemical analysis of sedimentary organic matter associated with uranium

Samples of sedimentary organic matter from several geologic environments and ages which are enriched in uranium (56 ppm to 12%) have been characterized. The three analytical techniqyes used to study the samples were Rock-Eval pyrolysis, pyrolysis-gas chromatography-mass spectrometry, and solid-state C-13 nuclear magnetic resonance (NMR) spectroscopy. In samples with low uranium content, the pyrolysis-gas chromatography products contain oxygenated functional groups (as hydroxyl) and molecules with both aliphatic and aromatic carbon atoms. These samples with low uranium content give measurable Rock-Eval hydrocarbon and organic-CO₂ yields, and C-13 NMR values of > 30% aliphatic carbon. In contrast, uranium-rich samples have few hydrocarbon pyrolysis products, increased Rock-Eval organic-CO₂ contents and > 70% aromatic carbon contents from C-13 NMR. The increase in aromaticity and decrease in hydrocarbon pyrolysis yield are related to the amount of uranium and the age of the uranium minerals, which correspond to the degree of radiation damage. The three analytical techniques give complementary results. Increase in Rock-Eval organic-CO₂ yield correlates with uranium content for samples from the Grants uranium region. Calculations show that the amount of organic-CO₂ corresponds to the quantity of uranium chemically reduced by the organic matter for the Grants uranium region samples.     

Proof of formation of organic matter in upper Devonian carbonate and carbonate-siliceous sediments of the South-Tatar uplift in constant photic layer anoxia

Samples of carbonate and siliceous-carbonate deposits of Semiluk—Sargaev horizons of the N?NE slope of the South Tatar uplift, Volga-Ural petroliferous basin, have been studied. Specific feature of the source rocks—high concentration of compounds—anoxia testifiers in the photic layer has been identified. That is, organic matter has been deposited under the conditions of the constant presence of anoxia in the photic layer of the sedimentation basin at sufficiently high thickness of the water column contaminated with hydrogen sulfide. Since by the composition of saturated hydrocarbons the studied samples are typical for deposits of the Semiluk horizon of the central part of the Volga-Ural basin, we can assume a fairly wide prevalence of such conditions within the South-Tatar arch. Changes in the concentrations of the components—anoxia markers—show cyclical changes in output layer contaminated with hydrogen sulfide or its bioproduction within the studied time.     

Effect of organic matter on DOM sorption on lake sediments

The effect of organic matter on the sorption of dissolved organic matter (DOM) on lake sediments is critical to understanding the fate and transport of contaminants at the sediment–water interface in lake ecosystems. Results indicate that DOM sorption on sediment is largely due to ligand exchange between the DOM and hydroxyl groups, and the amount of DOC sorbed is a linear function of added DOC. With increasing organic matter content the sediment has lower binding strength, higher releasing ability for DOM, and the higher amount of DOM sorbed by sediment naturally. There was no clear difference before and after the sediment was treated with H₂O₂, but the constant b implied that after the sediments were treated DOC release was promoted. Organic matter in the sediment tends to impede the sorption of DOC and results in a remarkable decrease in DOC sorption rates.     

多组分有机质作用下碳酸钙的矿化现象

采用SEM、XRD、FT-IR等手段对氨基酸、多糖以及有机酸混合体系中形成的碳酸钙晶体进行了表征,进而比较了多组分有机质作用下碳酸钙的矿化现象。结果表明,氨基酸-单糖体系(A-M)促进了碳酸钙的沉积,其钙化速率相较于对照组提高了36%;有机酸则抑制了碳酸钙的沉积,单糖-有机酸体系(M-O)、氨基酸-有机酸体系(A-O)和氨基酸-有机酸-单糖体系(A-O-M)的钙化速率分别下降了33%、29%、17%。其次,A-M体系合成的晶体以方解石为主,包含少量的球霰石,M-O、A-O和A-O-M体系则在柠檬酸的调控下合成了方解石。最后,A-M体系合成了块状晶体(粒径为10μm)及中空的环状晶体(粒径为5μm),而A-O和M-O体系合成了棒状晶体(长轴径5～15μm,短轴径3～5μm)。A-O-M体系存在含量最高的有机质,导致成核速率高于生长速率,因此合成的晶体呈粒状(粒径1～3μm)且发育不完整。研究揭示了多组分共存体系中的生物矿化现象,阐明了柠檬酸在多组分体系中对晶体成核及生长的主导调控作用,对研究黄龙高寒环境下的生物矿化机制具有重要意义。