NanoSIMS study of organic matter associated with soil aggregates: advantages, limitations, and combination with STXM

Direct observations of processes occurring at the mineral-organic interface are increasingly seen as relevant for the cycling of both natural soil organic matter and organic contaminants in soils and sediments. Advanced analytical tools with the capability to visualize and characterize organic matter at the submicrometer scale, such as Nano Secondary Ion Mass Spectrometry (NanoSIMS) and Scanning Transmission X-ray Microscopy (STXM) coupled to Near Edge X-ray Absorption Fine Structure Spectroscopy (NEXAFS), may be combined to locate and characterize mineral-associated organic matter. Taking advantage of samples collected from a decadal (15)N litter labeling experiment in a temperate forest, we demonstrate the potential of NanoSIMS to image intact soil particles and to detect spots of isotopic enrichment even at low levels of (15)N application. We show how microsites of isotopic enrichment detected by NanoSIMS can be speciated by STXM-NEXAFS performed on the same particle. Finally, by showing how (15)N enrichment at one microsite could be linked to the presence of microbial metabolites, we emphasize the potential of this combined imaging and spectroscopic approach to link microenvironment with geochemical process and/or location with ecological function.     

Model assessment of biogeochemical controls on dissolved organic carbon partitioning in an acid organic soil

A chemical model (constructed in the ORCHESTRA modeling framework) of an organic soil horizon was used to describe soil solution data (10 cm depth) and assess if seasonal variations in soil solution dissolved organic carbon (DOC) could be explained by purely abiotic (geochemical controls) mechanisms or whether factors related to biological activity are needed. The NICA-Donnan equation is used to describe the competitive binding of protons and cations and the charge on soil organic matter. Controls on organic matter solubility are surface charge and a parameter, gamma, that accounts for the distribution of humic molecules between hydrophobic and hydrophilic fractions. Calculations show that the variations in solute chemistry alone are not sufficient to account for the observed variations of DOC, but factors that alter gamma, such as biological activity, are. Assuming that DOC in organic soils is derived from soluble humic material and that gamma is modified seasonally due to biological activity (with monthly soil temperature used as a surrogate for biological activity) we are able to model the observed seasonality of soil solution DOC over a 10-year period. Furthermore, with modeled DOC coupled to other geochemical processes we also model soil solution pH and Al concentrations.     

Nitrogen and carbon dioxide adsorption by soils

High-resolution nitrogen (77 K) and carbon dioxide (273 K) adsorption at subatmospheric pressures has been studied for a range of model soils of various origins with different organic matter (OM) contents. It is demonstrated that N2 and CO2 molecules probe different regions of soil particles. Nitrogen is adsorbed primarily on the outer surface of soil particles, while CO2 has a higher affinity to OM domains. Low-pressure nitrogen adsorption reveals that soil particle surfaces consist of clay/mineral domains with discrete patches of OM. A linear correlation has been found between the CO2 uptake and the amount of organic carbon reduced per unit of the external surface area. A new method for discriminating the microporosity of soil particles and accessibility of OM has been proposed.     

The nature of soil organic matter affects sorption of pesticides. 1. Relationships with carbon chemistry as determined by 13C CPMAS NMR spectroscopy

The structural composition of soil organic matter (SOM) was determined in twenty-seven soils with different vegetation from several ecological zones of Australia and Pakistan using solid-state CPMAS 13C NMR. The SOM was characterized using carbon types derived from the NMR spectra. Relationships were determined between Koc (sorption per unit organic C) of carbaryl(1-naphthylmethylcarbamate) and phosalone (S-6-chloro-2,3-dihydro-2-oxobenzoxazol-3-ylmethyl O,O-diethyl phosphorodithioate) and the nature of organic matter in the soils. Substantial variations were revealed in the structural composition of organic matter in the soils studied. The variations in Koc values of the pesticides observed for the soils could be explained only when variations in the aromatic components of SOM were taken into consideration. The highly significant positive correlations of aromaticity of SOM and Koc values of carbaryl and phosalone revealed that the aromatic component of SOM is a good predictor of a soil's ability to bind such nonionic pesticides.     

Binding of ²³⁹Pu and ⁹⁰Sr to organic colloids in soil solutions: evidence from a field experiment

Colloidal transport has been shown to enhance the migration of plutonium in groundwater downstream from contaminated sites, but little is known about the adsorption of ??Sr and plutonium onto colloids in the soil solution of natural soils. We sampled soil solutions using suction cups, and separated colloids using ultrafiltration to determine the distribution of 23?Pu and ??Sr between the truly dissolved fraction and the colloidal fraction of the solutions of three Alpine soils contaminated only by global fallout from the nuclear weapon tests. Plutonium was essentially found in the colloidal fraction (>80%) and probably associated with organic matter. A significant amount of colloidal ??Sr was detected in organic-rich soil solutions. Our results suggest that binding to organic colloids in the soil solutions plays a key role with respect to the mobility of plutonium in natural alpine soils and, to a lesser extent, to the mobility of ??Sr.     

Zinc coordination to multiple ligand atoms in organic-rich surface soils

We report on the solid-phase speciation of naturally occurring Zn in metalliferous organic-matter-rich surface soils. Synchrotron-based studies were used to probe elemental distribution and associations in soil particles (micro-XRF) together with the mineralogy (micro-XRD) and Zn bonding environment (Zn-micro-XANES) at the micrometer-scale level. The average bonding environment of Zn was also probed for bulk soils using XANES. We found the distribution of elements within soil particles to be heterogeneous; however, some elements are consistently co-located. While conventional XRD analyses of whole soils did not identify any Zn mineral phase, synchrotron-based-micro-XRD analyses indicated that sphalerite (ZnS) is present in a particle from a wetland soil (soil labeled G3). Linear combination fit (LCF) analyses of XANES spectra collected for bulk soils (Zn-XANES) and microm-regions (Zn-micro-XANES) within soil particles suggest Zn bonds to oxygen-, nitrogen-, and sulfur-functional groups in these sulfur-, nitrogen-, and zinc-rich organic surface soils. The XANES spectra of all bulk soils and of all microm-regions except for the wetland soil (G3), where ZnS was the most significant constituent, were best fitted by the Zn-arginine reference compound and therefore seems to indicate Zn bonding to nitrogen. Thus, these results provide compelling evidence of the formation of highly covalent Zn-organic bonds in the organic-rich surface soils that were studied. This may explain in part why metal partition coefficients (Kd) are generally higher in organic soils, and why the toxic thresholds for total metal concentrations are higher in organic than in mineral soils.     

Zn speciation in the organic horizon of a contaminated soil by micro-X-ray fluorescence, micro- and powder-EXAFS spectroscopy, and isotopic dilution

Soils that have been acutely contaminated by heavy metals show distinct characteristics, such as colonization by metal-tolerant plant species and topsoil enrichment in weakly degraded plant debris, because biodegradation processes are strongly inhibited by contamination. Such an organic topsoil, located downwind of an active zinc smelter and extremely rich in Zn (approximately 2%, dry weight), was investigated by X-ray diffraction, synchrotron-based X-ray microfluorescence, and powder- and micro-extended X-ray absorption fine structure (EXAFS) spectroscopy for Zn speciation and by isotopic dilution for Zn lability. EXAFS spectra recorded on size fractions and on selected spots of thin sections were analyzed by principal component analysis and linear combination fits. Although Zn primary minerals (franklinite, sphalerite, and willemite) are still present (approximately 15% of total Zn) in the bulk soil, Zn was found to be predominantly speciated as Zn-organic matter complexes (approximately 45%), outer-sphere complexes (approximately 20%), Zn-sorbed phosphate (approximately 10%), and Zn-sorbed iron oxyhydroxides (approximately 10%). The bioaccumulated Zn fraction is likely complexed to soil organic matter after the plants' death. The proportion of labile Zn ranges from 54 to 92%, depending on the soil fraction, in agreement with the high proportion of organically bound Zn. Despite its marked lability, Zn seems to be retained in the topsoil thanks to the huge content of organic matter, which confers to this horizon a high sorption capacity. The speciation of Zn in this organic soil horizon is compared with that found in other types of soils.     

PAHs and organic matter partitioning and mass transfer from coal tar particles to water

The coal tar found in contaminated soils of former manufactured gas plants and coking plants acts as a long-term source of PAHs. Organic carbon and PAH transfer from coal tar particles to water was investigated with closed-looped laboratory column experiments run at various particle sizes and temperatures. Two models were derived. The first one represented the extraction process at equilibrium and was based on a linear partitioning of TOC and PAHs between coal tar and water. The partition coefficient was derived as well as the mass of extractable organic matter in the particles. The second model dealt with mass transfer. Particle diffusion was the limiting step; organic matter diffusivity in the coal tar was then computed in the different conditions. A good consistency was obtained between experimental and computed results. Hence, the modeling of PAH migration in contaminated soils at the field scale requires taking into account coal tar as the source-term for PAH release.     

Carbon speciation of diesel exhaust and urban particulate matter NIST standard reference materials with C(1s) NEXAFS spectroscopy

The U.S. National Institute of Standards and Technology (NIST) provides a number of particulate matter (PM) standard reference materials (SRM) for use in environmental and toxicological methodology and research. We present here the first analysis with respect to the molecular structure of the carbon in three such NIST SRM samples, i.e., diesel engine exhaust soot from heavy duty equipment engines (SRM 1650), diesel soot from a forklift engine (SRM 2975), and urban PM collected in St. Louis, MO (SRM 1648), with near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. The NEXAFS spectra of the two diesel soot samples appear quite similar, while they differ significantly from the urban PM spectrum, in agreement with X-ray diffraction data published recently. Such comparison is made in terms of aromatic and aliphatic carbon species, as well as by a general comparison with graphitic materials. Both diesel soot SRM samples contain basic graphitic structures, but the presence of exciton resonance and extended X-ray absorption fine structure oscillations in SRM 1650 and the lack therof in SRM 2975 suggest that SRM 1650 is the more graphitic material.The presence of polycyclic aromatic hydrocarbons, which have a characteristic NEXAFS resonance at the same position as graphite, can obscure the graphitic character of soot, unless an extraction of the organic matter is made. Our NEXAFS data do not suggest that the urban PM sample SRM 1648 contains a substantial amount of graphite-like material.     

Spectromicroscopy mapping of colloidal/particulate organic matter in Lake Brienz, Switzerland

Transmission electron microscopy (TEM), soft X-ray scanning transmission X-ray microscopy (STXM), and mu-FTIR spectromicroscopy were used to map colloidal/ particulate material in an ultra-oligotrophic lake, Lake Brienz, Switzerland, with a special focus on organic functionality. Within the statistical margin of error and the uncertainties arising from the representativeness of the results, the research reveals that organic material was associated with potassium-rich inorganic colloids present in surface and deep water (depths of 1 and 100 m, respectively), which indicates a vertical transfer of aggregates by sedimentation. Pure organic colloids could only be detected in surface waters. In addition, correlation map analysis of synchrotron-based mu-FTIR and carbon K-edge STXM spectromicroscopic data using spectra from the Lütschine and Aare Rivers as target spectra revealed spectral similarities with organic components from both tributary rivers in deeper regions (100 m) of the lake. The results prove that STXM and mu-FTIR can characterize colloidal and particulate organic material in low organic carbon systems.     

Interactions of DNA with clay minerals and soil colloidal particles and protection against degradation by DNase

Adsorption, desorption, and degradation by nucleases of DNA on four different colloidal fractions from a Brown soil and clay minerals were studied. The adsorption of DNase I and the structures of native DNA, adsorbed and desorbed, were also investigated by Fourier Transform Infrared (FTIR), circular dichroism (CD), and fluorescence spectroscopy, to determine the protection mechanism of DNA molecules by soil colloids and minerals against enzymatic degradation. Kaolinite exhibited the highest adsorption affinity for DNA among the examined soil colloids and clay minerals. In comparison with organomineral complexes (organic clays), DNA was tightly adsorbed by H2O2-treated clays (inorganic clays). FTIR spectra showed that the binding of DNA on kaolinite and inorganic clays changed its conformation from the B-form to the Z-form, whereas montmorillonite and organic clays retained the original B-form of DNA. A structural change from the B- to the C-form in DNA molecules desorbed from kaolinite was observed by CD spectroscopy and confirmed by fluorescence spectroscopy. The presence of soil colloids and minerals provided protection to DNA against degradation by DNase I. The higher level of protection was found with montmorillonite and organic clays compared to kaolinite and inorganic clays. The protection of DNA against nuclease degradation by soil colloids and minerals is apparently not controlled by the adsorption affinity of DNA molecules for the colloids and the conformational change of bound DNA. The higher stability of DNA seemed to be attributed mainly to the presence of organic matter in the system and the adsorption of nucleases on soil colloids and minerals. The information obtained in this study is of fundamental significance for the understanding of the behavior of extracellular DNA in soil environment.     

重庆典型烟区土壤团聚体中有机质及活性组分的分布特征

为有效调控植烟土壤肥力及合理进行田间碳素管理,采集了重庆彭水、丰都和巫山3个典型烟区的土壤样品。利用干筛法将土壤分成不同粒径的团聚体,分别用浓度33、167和333 mmol·L-1的KMnO₄溶液氧化处理,测定团聚体中高活性有机质(HLOM)、中活性有机质(MLOM)和活性有机质(LOM)含量(质量分数),并分析了各粒径团聚体中有机质及活性有机质的分布特征。结果表明,3个烟区土壤团聚体的组成均以1~2 mm的团聚体为主,占团聚体总量(质量分数)的40.16%~42.02%。除巫山烟区土壤0.25~0.50 mm团聚体含量(质量分数)显著高于彭水和丰都两个烟区外,其余粒径团聚体含量在3个典型烟区间的差异不显著(P>0.05)。随着粒径的增大,土壤团聚体中的总有机质(TOM)和LOM含量均降低,但HLOM和MLOM含量的变化因烟区的不同而异。在彭水和巫山烟区,HLOM和MLOM含量随团聚体粒径增大呈下降趋势,但在丰都烟区则表现为先降低后增加的变化趋势。土壤TOM、HLOM、MLOM和LOM在团聚体中的分布均以1~2 mm粒径最大,分别达29.99%~31.58%、24.29%~33.36%、24.15%~29.09%和18.46%~21.69%,因此将1~2 mm团聚体作为重庆市典型烟区的土壤有机质固定的特征团聚体。土壤TOM和LOM含量均分别与<0.25 mm团聚体中的TOM和LOM含量呈极显著正相关,表明该粒径团聚体有机质和活性有机质可以作为衡量重庆植烟土壤有机质含量变化动态的敏感性指标。      

Linking phosphorus sequestration to carbon humification in wetland soils by 31P and 13C NMR spectroscopy

Phosphorus sequestration in wetland soils is a prerequisite for long-term maintenance of water quality in downstream aquatic systems, but can be compromised if phosphorus is released following changes in nutrient status or hydrological regimen. The association of phosphorus with relatively refractory natural organic matter (e.g., humic substances) might protect soil phosphorus from such changes. Here we used hydrofluoric acid (HF) pretreatment to remove phosphorus associated with metals or anionic sorption sites, allowing us to isolate a pool of phosphorus associated with the soil organic fraction. Solution (31)P and solid state (13)C NMR spectra for wetland soils were acquired before and after hydrofluoric acid pretreatment to assess quantitatively and qualitatively the changes in phosphorus and carbon functional groups. Organic phosphorus was largely unaffected by HF treatment in soils dominated by refractory alkyl and aromatic carbon groups, indicating association of organic phosphorus with stable, humified soil organic matter. Conversely, a considerable decrease in organic phosphorus following HF pretreatment was detected in soils where O-alkyl groups represented the major fraction of the soil carbon. These correlations suggest that HF treatment can be used as a method to distinguish phosphorus fractions that are bound to the inorganic soil components from those fractions that are stabilized by incorporation into soil organic matter.     

Surface complexation of copper(II) on soil particles: EPR and XAFS studies

The interactions of transition metals with natural systems play an important role in the mobility and the bioavailability of these metals in soils. In this study, the adsorption of copper(II) onto natural soil particles was studied as a function of pH and metal concentration. The retention capacity of soil particles was determined at pH 6.2 to be equal to 6.7 mg of copper/g of solid. The Langmuir and Freundlich isotherm equations were then used to describe the partitioning behavior of the system at different pH values. A combination of EPR, extended X-ray absorption fine structure (EXAFS), and X-ray absorption near-edge structure (XANES) spectroscopies was used to probe the Cu atomic environment at the soil particles/aqueous interface. The spectroscopic study revealed that copper(II) ions are held in inner-sphere surface complexes. It also revealed that Cu was in an octahedral coordination with first-shell oxygen atoms. A weak tetragonal distortion was pointed out due to the Jahn-Teller effect, with a mean Cu-Oequatorial bond distance of 1.96 A and a Cu-Oaxial bond distance of 2.06 A. A detailed analysis of the spectroscopic data suggested that Cu(II) was bonded to organic matter coated onto the mineral fraction of soil particles.     

Electron microprobe and synchrotron x-ray fluorescence mapping of the heterogeneous distribution of copper in high-copper vineyard soils

The response of microorganisms to metal contamination of soils varies significantly from one investigation to another. One explanation is that metals are heterogeneously distributed at spatial scales relevant to microbes and that microoorganisms are able to avoid zones of intense contamination. This article aims to assess the microscale distribution of Cu in a vineyard soil. The spatial distribution of Cu was measured at two resolutions (0.3 mm and 20 microm) in thin sections of the surface 4 cm of undisturbed soil by electron microprobe and synchrotron X-ray microfluo-rescence spectroscopy. Bulk physicochemical analyses of Cu, pH, organic matter, texture, and mineralogy were performed. The results indicate that the Cu distribution is strongly heterogeneous at both scales of observation. Entire regions of the thin sections are virtually devoid of Cu, whereas highly localized "hotspots" have Cu signal intensities thousands of times higher than background. The distribution of Rb, or Al and Si, indicators of clay minerals, or Fe (iron (hydr)oxides), show that Cu is not preferentially associated with these mineral phases. Instead, Cu hotspots are associated with particulate organic matter. These observations suggest modification of current sampling protocols, and design of ecotoxicological experiments involving microorganisms, for contaminated soils.     

Modeling kinetics of Cu and Zn release from soils

Kinetics of Cu and Zn release from soil particles was studied using two surface soils with a stirred-flow method. Different solution pH, dissolved organic matter (DOM) concentrations, and flow rates were tested in this study. A model for kinetics controlled sorption/desorption reactions between soils and solutions was globally fit to all experimental data simultaneously. Results were compared to a model that assumes local instantaneous equilibrium. We obtained one unique set of model parameters applicable to different pH, dissolved organic carbon (DOC), and flow conditions. We included DOM complexation of copper ions, which decreased their sorption. The effect of pH was included by assuming proton competition with metal ions for binding sites on soil particles. These results provide the basis for developing predictive models for metal release from soil particles to surface waters and soil solution.     

Pesticides in western Canadian mountain air and soil

The distribution of organochlorine pesticides (OCP; in past and current use) in the mountains of western Canada was determined by sampling air, soil, and lichen along three elevational transects in 2003-2004. Two transects west of the Continental Divide were located in Mount Revelstoke and Yoho National Park, while the Observation Peak transect in Banff National Park is east of the divide. XAD-based passive air samplers, yielding annually averaged air concentrations, were deployed, and soils were collected at all 22 sampling sites, whereas lichen were only sampled in Revelstoke. Back trajectory analysis showed limited air mass transport from the Prairies to the east, but a high frequency of air arriving from the southwest, which includes agricultural regions in British Columbia and Washington State. Endosulfan, dieldrin, and a-hexachlorocyclohexane were the most prevalent OCPs in air and soil; hexachlorobenzene was only abundant in air; chlorothalonil, dacthal, and pentachloronitrobenzene were also consistently present. OCP air concentrations were similar across the three transects, suggesting efficient atmospheric mixing on a local and regional scale. Soil concentrations and soil/air concentration ratios of many OCPs were significantly higher west of the Continental Divide. The soil and lichen concentrations of most OCPs increased with altitude in Revelstoke, and displayed maxima at intermediate elevations at Yoho and Observation Peak. These distribution patterns can be understood as being determined by the balance between atmospheric deposition to, and retention within, the soils. Higher deposition, due to more precipitation falling at lower temperatures, likely occurs west of the divide and at higher elevations. Higher retention, due to higher soil organic matter content, is believed to occur in soils below the tree line. Highest pesticide concentrations are thus found intemperate mountain soils that are rich in organic matter and receive large amounts of cold precipitation.     

Receptor modeling of toronto PM2.5 characterized by aerosol laser ablation mass spectrometry

Urban Toronto fine particulate matter (PM2.5) was physically and chemically characterized by online aerosol laser ablation mass spectrometry (LAMS) between January 2002 and February 2003. The mass spectra from the analysis of individual aerosol particles were classified according to chemical composition by a neural network approach called adaptive resonance theory (ART-2a). Temporal trends of the hourly analysis rate of over 120 different particles types were constructed and subjected to positive matrix factorization (PMF). This receptor modeling technique enabled the identification of nine distinct emission sources responsible for these particle types: biogenic, mixed crustal, organic nitrate, construction dust, Toronto soil/road salt, secondary salt, wood burning, intercontinental dust, and an unknown source of aluminum fluoride dust. Episodic events occurred with the wood burning, intercontinental dust, and unknown dust sources. This is the first paper reporting the application of PMF to single-particle spectral data.     

Solid-solution partitioning of Cd, Cu, Ni, Pb, and Zn in the organic horizons of a forest soil

We report the solid-liquid partitioning of Cd, Cu, Ni, Pb, and Zn in 60 organic horizon samples of forest soils from the Hermine Watershed (St-Hippolyte, PQ, Canada). The mean Kd values are respectively 1132, 966, 802, 3337 and 561. Comparison of those Kd coefficients to published compilation values show that the Kd values are lower in acidic organic soil horizons relative to the overall mean Kd values compiled for mineral soils. But, once normalized to a mean pH of 4.4, the Kd values in organic soil horizons demonstrate the high sorption affinity of organic matter, which is either as good as or up to 30 times higher than mineral soil materials for sorbing trace metals. Regression analysis shows that, within our data set, pH and total metal contents are not consistent predictors of metal partitioning. Indeed, metal sorption by the solid phase must be studied in relation to complexation by dissolved organic ligands, and both processes may sometime counteract one another.     

Extended X-ray absorption fine structure spectroscopy evidence for the complexation of cadmium by reduced sulfur groups in natural organic matter

It is widely accepted that the bioavailability, toxicity, and mobility of trace metals are highly dependent on complexation reactions with functional groups in natural organic matter (NOM). In this study, the coordination chemistry of Cd in NOM was investigated by extended X-ray absorption fine structure spectroscopy. Soil organic matter (SOM) from different types of organic soils and dissolved organic matter (DOM) from an organic and a mineral soil horizon of a Spodosol and aquatic DOM from Suwannee River were investigated. In SOM samples (1000-25000 microg of Cd g(-1), pH 4.6-6.6), Cd was coordinated by 1.0-2.5 S atoms at a distance of 2.49-2.55 A and by 3.0-4.5 O/N atoms at a distance of 2.22-2.25 A. In DOM samples (1750-4250 microg of Cd g(-1), pH 5.4-6.3), Cd was coordinated by 0.3-1.8 S atoms at a distance of 2.51-2.56 A and 3.6-4.5 O/N atoms at a distance of 2.23-2.26 A. In both SOM and DOM samples a second coordination shell of 1.7-6.0 carbon atoms was found at an average distance of 3.12 A. This is direct evidence for inner-sphere complexation of Cd by functional groups in NOM. Furthermore, ion activity measurements showed that less than 1% of total Cd was in the form of free Cd2+ in our samples. Bond distances and coordination numbers suggest that Cd complexed in SOM and DOM is a mixture of a 4-coordination with S (thiols) and 4- and 6-coordinations with O/N ligands. Given that Cd-S associations on average are stronger than Cd-O/N associations, our results strongly indicate that reduced S ligands are involved in the complexation of Cd by NOM also at native concentrations of metal in oxidized organic-rich soils and in humic streams.