Molecular evaluation of soil organic matter characteristics in three agricultural soils by improved off-line thermochemolysis: The effect of hydrofluoric acid demineralisation treatment

Structural characterization using 2D NMR spectroscopy and TMAH-GC × GC-MS: Application to humic acids from soils of an integrated agricultural system and an Atlantic native forest

Understanding the chemical make-up of soils and their structure is critical for constraining the role of soil organic matter (SOM) into the global biogeochemical cycles, as well as to understand the capability of SOM to sequester carbon and mitigate greenhouse gas emissions. Here, we use two-dimensional ¹H-¹³C heteronuclear single quantum coherence nuclear magnetic resonance (2D ¹H-¹³C HSQC NMR) spectroscopy to structurally characterize the most refractory component of SOM, the humic acid (HA). The observations from 2D ¹H-¹³C HSQC NMR were coupled with lignin phenol and fatty acid measurements using tetramethylammonium hydroxide (TMAH) thermochemolysis - two-dimensional gas chromatography - mass spectrometry (TMAH-GC × GC-MS). We studied humic acids extracted from an integrated Crop - Livestock - Forest System (CLFS) agricultural area and an undisturbed Atlantic Native Forest (NF) area. We evaluated soils from two different depths: the topsoil (0-20 cm) and subsoil (60-100 cm) layers, and reveal the presence of oxidized ligninaceous phenols as we had previously hypothesized. Collectively, our results indicate that there are significant oxidative processes with increasing soil depth which are more pronounced in the CLFS relative to the NF area. Degradation of stearic acid with increasing depth in the CLFS soils indicated that the CLFS is more microbiologically active than NF. Therefore, CLFS is less biochemically stable than we originally perceived. The enhanced bio-reactivity of CLFS is likely driving the enhanced carbon sequestration in the CLFS soils. This is perhaps due to the diversity of biomass remnants available at the CLFS soil rhizosphere which allows for more different types of biomass to be sequestered as oxidized ligninaceous phenols. Our results employing structural characterization with 2D ¹H-¹³C HSQC NMR and TMAH-GC × GC-MS provide a new layer of knowledge about the practice of integrated agricultural systems and allow us to understand the structure and fate of sequestered carbon in soils from different soil environments.

Molecular properties of the Humeome of two calcareous grassland soils as revealed by GC/qTOF-MS and NMR spectroscopy

A Humeomic fractionation revealed the humus molecular composition of two uncropped calcareous soils of Northern France and differentiated the soils Humeome by extracting humic components first unbound to the organo-mineral matrix and then liberated from their progressively stronger intermolecular and intramolecular ester and ether linkages. We separated organo- (ORG1-3) and water-soluble (AQU2 and AQU4) fractions, a final extractable fraction (RESOM) and soil residues. Organo-soluble fractions were studied by GC coupled with high-resolution mass spectrometry (GC/qTOF-MS), all fractions underwent mono- and two-dimensional liquid-state NMR (except for the iron-rich AQU4 fraction), while solid-state ¹³C-CPMAS-NMR spectroscopy analyzed soil residues. The Calcaric Leptosol (A) showed a larger mass extraction than the Calcaric Cambisol (B), and a greater cumulative C and N content in its Humeome. Both soils showed the greatest weight yield for AQU4 fraction, followed by ORG2, RESOM, ORG1, AQU2, and ORG3. ORG2 was the most differentiating fraction between the two soils for both compound concentration and diversity, showing a larger C content for soil A than for soil B and a different distribution in aromatic compounds, fatty acids, and dicarboxylic acids. No significant differences between soils were found for ORG 3, suggesting similar processes of OM stabilization for its recalcitrant components, mostly hydrophobic esters of alkanoic, hydroxy, and aromatic acids with linear alkanols. We confirmed that Humeomic fractionation coupled to advanced analytical instrumentations enabled a detailed molecular characterization of the soil Humeome and differentiated between the two calcareous grassland soils and the other soils previously subjected to Humeomics.

Use of Thermally Assisted Hydrolysis and Methylation (THM-GC-MS) to Unravel Influence of Pottery Production and Post-Depositional Processes on the Molecular Composition of Organic Matter in Sherds from a Complex Coastal Settlement

Ceramic fragments from the Islet of Guidoiro Areoso (NW Spain), covering a wide range of cultural periods (Neolithic to Late Bronze Age), have been studied by color analysis, elemental analysis of carbon (C) and nitrogen (N), and molecular analysis (thermally assisted hydrolysis and methylation, THM-GC-MS), in order to identify the organic matter (OM) in the prehistoric pottery and reveal information on ceramic production techniques, food remains and post-depositional effects. Results showed that the strong marine influence (sherds recovered from coastal deposits) and microbial activity (recovery from waste deposits, “cuncheiros”) had a profound effect on C/N ratio and molecular composition (N-rich protein and chitin structures). Other organic ingredients originated from the material used for creating the ware (detected as pyrogenic OM) and possibly food remains (fatty acid fingerprints). Dark-colored ware was enriched in both pyrogenic OM from incomplete combustion and non-bacterial fatty acids. Fatty acid patterns could not be related to possible vessel use, and markers of aquatic resources were scarce, or absent. It is argued that THM-GC-MS of pottery fragments is useful for understanding how an archaeological deposit developed in time, what kinds of OM are present, and possibly to make a pre-selection of samples with high potential for more cost-demanding dietary molecular assessments.

Hydrochar obtained with by-products from the sugarcane industry: Molecular features and effects of extracts on maize seed germination

Sugarcane bagasse, vinasse and a mixture of sugarcane bagasse and vinasse were hydrothermally carbonized (HTC), with and without the addition of phosphoric acid, in order to propose new applications of sucroenergetic industry by-products on soil. Detailed information on the composition and properties of hydrochars has been obtained through elemental composition, thermogravimetric analysis, nuclear magnetic resonance and, thermochemolysis GC-MS. The soluble acidic fraction from the hydrochar samples were applied to maize seeds to evaluate the agronomic potential as biostimulants and relate the molecular features with maize seed germination. The HTC treatment converted polysaccharide-based biomasses into hydrochars with hydrophobic characteristics (C-Aryl and C-Akyl). Furthermore, the addition of phosphoric acid further increased the overall hydrophobicity and shifted the thermal degradation of the hydrochars to higher temperatures. Biomass influenced the hydrochars that formed, in which the molecular features of sugarcane bagasse determined the formation of more polar hydrochar, due to the preservation of lignin and phenolic components. Meanwhile, the HTC of vinasse resulted in a more hydrophobic product with an enrichment of condensed and recalcitrant organic fractions. The germination assay showed that polar structures of bagasse may play a role in improving the maize seeds germination rate (increase of ~11%), while the hydrophobic domains showed negative effects. The responses obtained in germination seems to be related to the molecular characteristics that organic extracts can present in solution.

Deciphering organic matter sources and ecological shifts in blue carbon ecosystems based on molecular fingerprinting

Blue carbon ecosystems (BCE) play an essential role in the global carbon cycle by removing atmospheric carbon dioxide and storing it as organic carbon (OC) in biomass and sediments. However, organic matter (OM) deposition and degradation/preservation processes are poorly understood, especially on the long-term and at molecular scales. We analysed sediment samples from six cores collected in tidal marshes, mangroves and seagrasses (up to 150 cm long cores spanning up to 10,000 yrs of OC accumulation) from Spencer Gulf (South Australia), by pyrolysis (Py-GC-MS and THM-GC-MS), and we compared the results with elemental and stable isotope data, to decipher OM provenance and to assess degradation/preservation dynamics. The results showed that: (1) the major biopolymers preserved were polysaccharides, polyphenolic moieties (lignin and tannin) and polymethylenic moieties (e.g. cutin, suberin, chlorophyll) with smaller apportions of proteins and resins; (2) the OM originates predominantly from vascular plant materials (in particular lignocellulose) that have been well-preserved, even in some of the oldest sediments; (3) mangroves were found to be the most efficient OC sinks, partially explained by syringyl lignin preservation; (4) seagrasses were shown to store polysaccharide-enriched OM; (5) large proportions of polycyclic aromatic hydrocarbons (PAHs) in surficial tidal marsh and mangrove sediments probably reflect pyrogenic OM from industrial combustion, and; (6) "ecosystem shifts", i.e. mangrove encroachment in tidal marsh and transition from seagrass to mangrove, were detected. Deposition environment and source vegetation control OC sequestration and there is no specific recalcitrant form of OM that is selectively preserved. For the first time, we demonstrate how analytical pyrolysis in combination with stable isotope analysis can be used to reconstruct (palaeo-)ecological shifts between different BCE. This study improves our knowledge on OC accumulation dynamics and the response of BCE to environmental change, which can inform the implementation of strategies for climate change mitigation.

Bioactivity of humic substances and water extracts from compost made by ligno-cellulose wastes from biorefinery

The ligno-cellulose residues from biorefinery production of bio-ethanol were used as woody structuring material within an on-farm composting system, with the aim to obtain bioactive water soluble and humic fractions from composted materials. The molecular characterization of initial biomasses and final products revealed a transformation towards more stable compounds during composting and showed the selective incorporation of specific phenolic derivatives of ligno-cellulose in both bulk samples and corresponding extracts. While the use of the stable bulk composts as organic fertilizer resulted in a decrease of nitrogen and phosphorous assimilation in maize tissues, a bio-stimulation was shown by water soluble organic compounds and humic substances in germination tests and pot experiments, respectively. The differential responses obtained in maize seedlings and plants were related to the molecular composition and concentration of the applied water extracts and humic substances, thus suggesting a role of phenols and lignin derivatives in the stimulation of maize roots and shoots and the enhancement of P uptake. The results confirm that ligno-cellulose residues may be effectively recycled as composting additives in order to enrich mature compost in aromatic and lignin compounds. A preliminary knowledge on the molecular characteristics and biological properties of composted materials is an essential requirement to select the most suitable derivatives from composted ligno-cellulose wastes in sustainable agricultural practices.

Protection of extractable lipid and lignin: Differences in undisturbed and cultivated soils detected by molecular markers

Understanding formation of organo-mineral association is crucial for soil organic matter (SOM) stabilization. To remove reactive minerals from un-disturbed natural soil (NS) and two cultivated soils (dry-farming soil, TD, and terrace paddy soil, TP), a 10% HF/1M HCl treatment was applied. The mineral protection of different molecular SOM structures before and after cultivation was compared by using markers for lipid and lignin. The removal of reactive mineral increased the lipid extractability in TD and NS similarly, indicating that the cultivation did not reduce the mineral protection; this is attributable to fertilizer application and amorphous Fe oxide enrichment. In TP, the extent of lipid protection was lower than in TD, demonstrating that the protection depends on the type of cultivation. In contrast to lipids, lignin-derived phenols decreased over 80% after acid treatment. Furthermore, the ratios of acid to aldehyde in vanillyl ((Ad/Al)_V) of TD and TP were much higher than in NS, indicating an increased oxidation of lignin in cultivated soils. During acid treatment, two distinct layers of soil particles were identified: an organic matter (OM)-enriched layer (L_OM), and a non-reactive mineral-enriched layer (L_NR) with hardly detectable OC content. However, up to 50% of lipids were detected in L_NR, indicating that lipids did not selectively interact with reactive mineral particles. In TD and TP, (Ad/Al)_V values were higher in L_OM than in L_NR, indicating a strong interaction of oxidized lignin in L_OM. Therefore, the protection of lignin, especially highly oxidized lignin, can depend more on reactive minerals than lipid. Promoting the formation of organo-mineral complexes is the primary strategy for soil management, especially for highly oxidized OM.

Composition of dissolved organic matter (DOM) from periodically submerged soils in the Three Gorges Reservoir areas as determined by elemental and optical analysis, infrared spectroscopy, pyrolysis-GC-MS and thermally assisted hydrolysis and methylation

Soil-derived dissolved organic matter (DOM) has a major influence in biogeochemical processes related to contaminant dynamics and greenhouse gas emissions, due to its reactivity and its bridging role between the soil and aquatic systems. Within the Three Gorges Reservoir (TGR, China) area, an extensive water-fluctuation zone periodically submerges the surrounding soils. Here we report a characterization study of soil-derived DOM across the TGR areas, using elemental and optical analysis, infrared spectroscopy (FTIR), pyrolysis-GC-MS (Py-GC-MS) and thermally assisted hydrolysis and methylation (THM-GC-MS). The results showed that the soil DOM from the TGR area is a mixture of "allochthonous" (i.e., plant-derived/terrigenous) and "autochthonous" (i.e., microbial) origins. The terrigenous DOM is composed primarily of phenolic and aliphatic structures from lignin and aliphatic biopolymers (i.e. cutin, suberin), respectively. Multivariate statistics differentiated between two fractions of the microbial DOM, i.e. chitin-derived, perhaps from fungi and arthropods in soil, and protein-derived, partially sourced from algal or aquatic organisms. Molecular proxies of source and degradation state were in good agreement with optical parameters such as SUVA₂₅₄, the fluorescence index (FI) and the humification index (HIX). The combined use of elemental analysis, fluorescence spectroscopy, and Py-GC-MS provides rigorous and detailed DOM characterization, whereas THM-GC-MS is useful for more precise but qualitative identification of the different phenolic (cinnamyl, p-hydroxyphenyl, guaiacyl, syringyl and tannin-derived) and aliphatic materials. With the multi-methodological approach used in this study, FTIR was the least informative, in part, because of the interference of inorganic matter in the soil DOM samples. The soil DOM from the TGR's water fluctuation zone exhibited considerable compositional diversity, mainly related to the balance between DOM source (microbial- or plant-derived), local vegetation and anthropogenic activities (e.g., agriculture). Finally, the relationship between DOM composition and its potential reactivity with substances of environmental concerns in the TGR area are also discussed.

Application of DRIFTS, 13C NMR, and py-MBMS to Characterize the Effects of Soil Science Oxidation Assays on Soil Organic Matter Composition in a Mollic Xerofluvent

Chemical oxidations are routinely employed in soil science to study soil organic matter (SOM), and their interpretation could be improved by characterizing oxidation effects on SOM composition with spectroscopy. We investigated the effects of routinely employed oxidants on SOM composition in a Mollic Xerofluvent representative of intensively managed agricultural soils in the California Central Valley. Soil samples were subjected to oxidation by potassium permanganate (KMnO₄), sodium hypochlorite (NaOCl), and hydrogen peroxide (H₂O₂). Additionally, non-oxidized and oxidized soils were treated with hydrofluoric acid (HF) to evaluate reduction of the mineral component to improve spectroscopy of oxidation effects. Oxidized non-HF and HF-treated soils were characterized by diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), ¹³C cross polarization magic angle spinning (CP-MAS) nuclear magnetic resonance (NMR) spectroscopy, and pyrolysis molecular beam mass spectrometry (py-MBMS), and for particle size distribution (PSD) using laser diffractometry (LD). Across the range of soil organic carbon (OC) removed by oxidations (14-72%), aliphatic C-H stretch at 3000-2800 cm^-1 (DRIFTS) decreased with OC removal, and this trend was enhanced by HF treatment due to significant demineralization in this soil (70%). Analysis by NMR spectroscopy was feasible only after HF treatment, and did not reveal trends between OC removal and C functional groups. Pyrolysis-MBMS did not detect differences among oxidations, even after HF treatment of soils. Hydrofluoric acid entailed OC loss (13-39%), and for H₂O₂ oxidized soils increased C:N and substantially decreased mean particle size. This study demonstrates the feasibility of using HF to improve characterizations of SOM composition following oxidations as practiced in soil science, in particular for DRIFTS. Since OC removal by oxidants, mineral removal by HF, and the interaction of oxidants and HF observed for this soil may differ for soils with different mineralogies, future work should examine additional soil and land use types to optimize characterizations of oxidation effects on SOM composition.

A molecular zoom into soil Humeome by a direct sequential chemical fractionation of soil

A Humeomics sequential chemical fractionation coupled to advanced analytical identification was applied directly to soil for the first time. Humeomics extracted ~235% more soil organic carbon (SOC) than by the total alkaline extraction traditionally employed to solubilise soil humic molecules (soil Humeome). Seven fractions of either hydro- or organo-soluble components and a final unextractable humic residue were separated from soil. These materials enabled an unprecedented structural identification of solubilised heterogeneous humic molecules by combining NMR, GC-MS, and ESI-Orbitrap-MS. Identified molecules and their relative abundance were used to build up structure-based van Krevelen plots to show the specific contribution of each fraction to SOC. The stepwise isolation of mostly hydrophobic and unsaturated molecules of progressive structural complexity suggests that humic suprastructures in soil are arranged in multi-molecular layers. These comprised molecules either hydrophobically adsorbed on soil aluminosilicate surfaces in less stable fractions, or covalently bound in amorphous organo-iron complexes in more recalcitrant fractions. Moreover, most lipid molecules of the soil Humeome appeared to derive from plant polyesters rather than bacterial metabolism. An advanced understanding of soil humic molecular composition by Humeomics may enable control of the bio-organic dynamics and reactivity in soil.

Rapid screening of phytoremediation effluents by off-line tetramethylammonium hydroxide assisted thermochemolysis

Tetramethylammonium hydroxide-assisted thermochemolysis performed in an off-line mode proved a useful tool in determining organic compounds in the effluent from laboratory-scale phytoremediation systems. Studies were performed with artificial wastewaters contaminated with xylenols and densely rooted Juncus effuses plants. Analytes in these molecular-level based studies included xylenol substrates, an array of stable intermediates such as low molecular weight carboxylic acids and oxidative coupling products (tetramethyl biphenyldiols, tetramethyl diphenylether monools), diagnostic fatty acid biomarkers, as well as lignin-, carbohydrate-, and protein-based phenols and carboxylic acids. Lignin-based breakdown products belonged to p-hydroxyphenyl- and guaiacyl-units, with lower abundance of syringyl units and the dominance of acids over phenols. Monomeric lignin-, protein- and carbohydrate-based breakdown products could not be detected in the non-treated lyophilized effluent. The formation of diketopiperazines pointed to soluble peptides and proteins. The procedure described herein can easily be applied in every modern laboratory to characterize underlying processes in phytoremediation.

Molecular characteristics of humic acids isolated from vermicomposts and their relationship to bioactivity

Vermitechnology is an effective composting method, which transforms biomass into nutrient-rich organic fertilizer. Mature vermicompost is a renewable organic product containing humic substances with high biological activity. The aim of this study was to assess the chemical characteristics and the bioactivity of humic acids isolated from different vermicomposts produced with either cattle manure, sugar cane bagasse, sunflower cake from seed oil extraction, or filter cake from a sugar cane factory. More than 200 different molecules were found, and it was possible to identify chemical markers on humic acids according to the nature of the organic source. The large hydrophobic character of humic extracts and the preservation of altered lignin derivatives confer to humic acids the ability to induce lateral root emergence in maize seedlings. Humic acid-like substances extracted from plant biomass residues represent an additional valuable product of vermicomposting that can be used as a plant growth promoter.