Chemical characterization of dissolved organic matter in moist acidic tussock tundra soil using ultra-high resolution 15T FT-ICR mass spectrometry

Research progress on the characteristics, sources, and environmental and potential health effects of water-soluble organic compounds in atmospheric particulate matter

Water-soluble organic compounds (WSOCs) have received extensive attention due to their indistinct chemical components, complex sources, negative environmental impact, and potential health effects. To the best of our knowledge, until now, there has been no comprehensive review focused on the research progress of WSOCs. This paper reviewed the studies on chemical constituent and characterization, distribution condition, sources, environmental impact, as well as the potential health effects of WSOCs in the past 13 years. Moreover, the main existing challenges and directions for the future research on WSOCs were discussed from several aspects. Because of the complex composition of WSOCs and many unknown individual components that have not been detected, there is still a need for the identification and quantification of WSOCs. As modern people spend more time in indoor environments, it is meaningful to fill the gaps in the component characteristics and sources of indoor WSOCs. In addition, although in vitro cell experiments have shown that WSOCs could induce cellular oxidative stress and trigger the inflammatory response, the corresponding mechanisms of action need to be further explored. The current population epidemiology research of WSOCs is missing. Prospectively, we propose to conduct a comprehensive and simultaneous analysis strategy for concentration screening, source apportionment, potential health effects, and action mechanisms of WSOCs based on high throughput omics coupled with machine learning simulation and prediction.

Implications of the Cultivation of Rosemary and Thyme (Lamiaceae) in Plant Communities for the Development of Antioxidant Therapies

Oxidative stress is the most critical factor in multiple functional disorders' development, and natural antioxidants could protect the human body against it. Our study aims to investigate the polyphenol content of four extracts of two medicinal plants (Rosmarinus officinalis L. and Thymus vulgaris L.) and analyze the correlation with their antioxidant activity. The research was carried out on extracts of rosemary and thyme obtained from species cultivated together in plant communities. Both were compared with extracts from species cultivated in individual crops (control crops). Their polyphenols were determined by spectrophotometric methods (dosage of flavones, phenol carboxylic acids, and total polyphenols) and chromatography (UHPLC-MS and FT-ICR MS). Triterpenic acids were also quantified, having a higher concentration in the thyme extract from the culture. The antioxidant activity of the dry extracts was evaluated in vitro (DPPH, ABTS, and FRAP) and in silico (prediction of interactions with BACH1/BACH2 transcription factors). The concentrations of polyphenols are higher in the extracts obtained from the sources collected from the common crops. These observations were also validated following the chromatographic analysis for some compounds. Statistically significant differences in the increase in the antioxidant effect were observed for the extracts from the common batches compared to those from the individual ones. Following the Pearson analysis, the IC₅₀ values for each plant extract were strongly correlated with the concentration of active phytoconstituents. Molecular docking studies revealed that quercetin could bind to BTB domains of BACH1 and BACH2 transcription factors, likely translating into increased antioxidant enzyme expression. Future studies must validate the in silico findings and further investigate phytosociological cultivation's effects.

Molecular insights into the chemodiversity of dissolved organic matter and its interactions with the microbial community in eco-engineered bauxite residue

Dissolved organic matter (DOM) plays an important role in the biogeochemical function development of bauxite residue. Nevertheless, the DOM composition at the molecular level and its interaction with microbial community during soil formation of bauxite residue driven by eco-engineering strategies are still relatively unknown. In the present study, the DOM composition at the molecular level and its interactions with the microbial community in amended and revegetated bauxite residue were explored. The results showed that the amendment applications and revegetation enhanced the accumulation of unsaturated molecules with high values of double bond equivalent (DBE) and nominal oxidation of carbon (NOSC) and aromatic compounds with high values of modified aromaticity index (AI_mod) as well as the reduction of average weighted molecular mass of DOM molecules. Significant correlations between DOM molecules and the microbial community and Fe/Al oxides were found. DOM molecules were decomposed by the microbial community and sequestered onto Fe/Al oxides, which were the main driving factors that changed DOM chemodiversity in the amended and revegetated bauxite residue. These findings are beneficial for understanding the biogeochemical behaviours of DOM and providing a critical basis for the development of eco-engineering strategies towards soil formation and the sustainable revegetation of bauxite residue.

Molecular transformation of organic nitrogen in Antarctic penguin guano-affected soil

Organic nitrogen (ON) is an important participant in the Earth's N cycle. Previous studies have shown that penguin feces add an abundance of nutrients including N to the soil, significantly changing the eco-environment in ice-free areas in Antarctica. To explore the molecular transformation of ON in penguin guano-affected soil, we collected guano-free weathered soil, modern guano-affected soil from penguin colonies, ancient guano-affected soil from abandoned penguin colonies, and penguin feces from the Ross Sea region, Antarctica, and Fourier transform ion cyclotron mass spectrometry (FT-ICR MS) was used to investigate the chemical composition of water-extractable ON. By comparing the molecular compositions of ON among different samples, we found that the number of ON compounds (>4,000) in weathered soil is minimal, while carboxylic-rich alicyclic-like molecules (CRAM-like) are dominant. Penguin feces adds ON into the soil with > 10,000 CHON, CHONS and CHN compounds, including CRAM-like, lipid-like, aliphatic/ peptide-like molecules and amines in the guano-affected soil. After the input of penguin feces, macromolecules continue to degrade, and other ON compounds tend to be oxidized into relatively stable CRAM-like molecules, this is an important transformation process of ON in guano-affected soils. We conclude the roles of various forms of ON in the N cycle are complex and diverse. Combined with previous studies, ON eventually turns into inorganic N and is lost from the soil. The lost N ultimately returns to the ocean and the food web, thus completing the N cycle. Our study preliminarily reveals the molecular transformation of ON in penguin guano-affected soil and is important for understanding the N cycle in Antarctica.

Characterization of biochar-derived organic matter extracted with solvents of differing polarity via ultrahigh-resolution mass spectrometry

In recent years, biochar, a porous carbon-based material, has gained attention for its application prospects in contaminated soil remediation and soil improvement. Biochar-derived organic matter has a key role in influencing the migration and transformation of soil elements and pollutants. However, existing research concerning the molecular characteristics of biochar-derived organic matter is limited. Here, we used four polar solvents - dichloromethane (CH₂Cl₂), acetone (CH₃COCH₃), methanol (CH₃OH), and distilled water (H₂O) - to extract organic matter from soybean straw biochar and wheat straw biochar by accelerated solvent extraction (ASE). We characterized the extracts using Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). We found considerable differences in organic matter according to the extraction solvents; such differences were related to the polarity of the solvent, as well as intermolecular forces between the solvent and organic matter. CH₃OH extracted the most biochar-extractable organic matter components because CH₃OH can weaken or destroy oxygen bridge bonds in biochar and form hydrogen bonds with small-molecule organic compounds. CH₃OH and H₂O have strong extraction capacity for compounds containing heteroatoms. CH₂Cl₂-extractable organic matter is relatively labile and bioavailable, while CH₃OH- and H₂O-extractable organic matters are relatively stable. In addition, the binding capacity of biochar-derived organic matter for minerals and pollutants differed among fractions, in part because of differences in molecular weight, atomic O/C and H/C ratios, heteroatom distribution, and biomolecular compounds present in biochar-derived organic matter. The findings in this study help to select appropriate extractants to analyze biochar-derived organic matter for various research purposes, and provides a theoretical basis for biochar-based remediation of contaminated soil.

Decreasing molecular diversity of soil dissolved organic matter related to microbial community along an alpine elevation gradient

Characterization of soil dissolved organic matter (DOM) and understanding of the interactions between soil microbial communities and DOM molecules along elevation gradients in alpine ecosystems are still limited. To unravel these interactions and how they change along alpine elevation gradients, we sampled topsoil in the Sygera Mountains (Tibet, China) at elevations between 3800 and 4600 m. The molecular characteristics of soil DOM were determined using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and soil microbial composition was identified by high-throughput sequencing. Among the seven components of DOM, the lignins/CRAM (carboxyl-rich alicyclic molecules)-like structure dominated at all elevations, followed by tannins, while the relative abundance of unstable substances, including lipids, aliphatic/protein, and carbohydrates, was lower. As elevation increased, the molecular diversity, degree of oxidation, aromaticity, and unsaturation of soil DOM decreased. The abundance and diversity of soil bacteria and fungi also generally decreased with elevation. Both bacteria and fungi play an important role in the degradation of DOM molecules, but bacteria appear to have greater degradation ability. Among them, Proteobacteria and Bacteroidetes mainly promote the degradation of lignins/CRAM-like structure molecules, while Basidiomycota mainly degrade more unstable substrates. Co-occurrence network analysis revealed complex correlations between specific microbial groups and DOM molecules. Our results suggest that more active cycling of soil DOM could occur in alpine ecosystems due to climate warming, as the result of increased vegetation productivity and litter input in response to rising temperature promoting the relative abundance of microbial groups capable of degrading lignins/CRAM-like structures in soil DOM.

Analysis of environmental organic matters by Ultrahigh-Resolution mass spectrometry-A review on the development of analytical methods

Owing to the increasing environmental and climate changes globally, there is an increasing interest in the molecular-level understanding of environmental organic compound mixtures, that is, the pursuit of complete and detailed knowledge of the chemical compositions and related chemical reactions. Environmental organic molecule mixtures, including those in air, soil, rivers, and oceans, have extremely complex and heterogeneous chemical compositions. For their analyses, ultrahigh-resolution and sub-ppb level mass accuracy, achievable using Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS), are important. FT-ICR MS has been successfully used to analyze complex environmental organic molecule mixtures such as natural, soil, particulate, and dissolved organic matter. Despite its success, many limitations still need to be overcome. Sample preparation, ionization, structural identification, chromatographic separation, and data interpretation are some key areas that have been the focus of numerous studies. This review describes key developments in analytical techniques in these areas to aid researchers seeking to start or continue investigations for the molecular-level understanding of environmental organic compound mixtures.

High Molecular Diversity of Organic Nitrogen in Urban Snow in North China

Snow serves as a vital scavenging mechanism to gas-phase and particle-phase organic nitrogen substances in the atmosphere, providing a significant link between land-atmosphere flux of nitrogen in the surface-earth system. Here, we used optical instruments (UV-vis and excitation-emission matrix fluorescence) and a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) to elucidate the molecular composition and potential precursors of snow samples collected simultaneously at four megacities in North China. The elemental O/N ratio (≥3), together with the preference in the negative ionization mode, indicates that the one and two nitrogen atom-containing organics (CHON₁ and CHON₂) in snow were largely in the oxidized form (as organic nitrates, -ONO₂). This study assumed that scavenging of particle-phase and gas-phase organic nitrates might be significant sources of CHON in precipitation. A gas-phase oxidation process and a particle-phase hydrolysis process, at a molecular level, were used to trace the potential precursors of CHON. Results show that more than half of the snow CHON molecules may be related to the oxidized and hydrolyzed processes of atmospheric organics. Potential formation processes of atmospheric organics on a molecular level provide a new concept to better understand the sources and scavenging mechanisms of organic nitrogen species in the atmosphere.

Application of Fourier transform ion cyclotron resonance mass spectrometry in deciphering molecular composition of soil organic matter: A review

Swiftly deciphering soil organic matter (SOM) composition is critical for research on soil degradation and restoration. Recent advances in analytical techniques (e.g., optical methods and mass spectrometry) have expanded our understanding of the composition, origin, and evolution of SOM. In particular, the use of Fourier transform ion cyclotron resonance mass spectrometers (FTICR-MS) makes it possible to interpret SOM compositions at the molecular level. In this review, we discuss extraction, enrichment, and purification methods for SOM using FTICR-MS analysis; summarize ionization techniques, FTICR-MS mechanisms, data analysis methods, and molecular compositions of SOM in different environments (providing new insights into its origin and evolution); and discuss factors affecting its molecular diversity. Our results show that digenesis, combustion, pyrolysis, and biological metabolisms jointly contribute to the molecular diversity of SOM molecules. The SOM thus formed can further undergo photodegradation during transportation from land to fresh water (and subsequently oceans), resulting in the formation of dissolved organic matter (DOM). Better understanding the molecular features of DOM therefore accelerates our understanding of SOM evolution. In addition, we assess the degradation potential of SOM in different environments to better inform soil remediation methods. Finally, we discuss the merits and drawbacks of applying FTICR-MS on the analysis of SOM molecules, along with existing gaps in knowledge, challenges, and new opportunities for research in FTICR-MS applications and SOM identification.

MFAssignR: Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures

Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements. Accurate and efficient characterization of these mixtures is critical to being better able to evaluate their effect on human health and climate. This characterization requires accurate mass signals free from isobaric interferences, instrument noise, and mass measurement biases, allowing for molecular formula identification. To address this need, an open source post-processing pipeline for ultrahigh resolution mass spectra of environmental complex mixtures software was developed. MFAssignR contains functions that perform noise estimation, ¹³C and ³⁴S polyisotopic mass filtering, mass measurement recalibration, and molecular formula assignment as part of a consistent data processing environment. Novel applications of mass defect analysis were used in the functions for noise estimation and isotope pair identification. Using formula extensions, exact mass measurements are converted to unambiguous molecular formulas via data dependent pathways, reducing a priori decisions. Optional molecular formula ambiguity and multiple non-oxygen heteroatoms are provided for custom user applications, including isotopically labeled reactive species, halogen-containing species, or tandem ultrahigh resolution mass spectrometry. This represents uncommon flexibility for an open-source software package. To evaluate the performance of MFAssignR, it was used to characterize a sample of biomass burning influenced organic aerosol and the results were compared to those from other available methods of molecular formula assignment and noise estimation. The differences between the methods are described here. Overall, the inclusion of a full pipeline of data preparation functions and the data-dependent ambiguity reductions in MFAssignR render excellent results and make MFAssignR well-suited for the consistent and efficient analysis of environmental complex mixtures. MFAssignR is publicly available via GitHub.

Single-Cell Metabolic Profiling: Metabolite Formulas from Isotopic Fine Structures in Heterogeneous Plant Cell Populations

Characterization of the metabolic heterogeneity in cell populations requires the analysis of single cells. Most current methods in single-cell analysis rely on cell manipulation, potentially altering the abundance of metabolites in individual cells. A small sample volume and the chemical diversity of metabolites are additional challenges in single-cell metabolomics. Here, we describe the combination of fiber-based laser ablation electrospray ionization (f-LAESI) with 21 T Fourier transform ion cyclotron resonance mass spectrometry (21TFTICR-MS) for in situ single-cell metabolic profiling in plant tissue. Single plant cells infected by bacteria were selected and sampled directly from the tissue without cell manipulation through mid-infrared ablation with a fine optical fiber tip for ionization by f-LAESI. Ultrahigh performance 21T-FTICR-MS enabled the simultaneous capture of isotopic fine structures (IFSs) for 47 known and 11 unknown compounds, thus elucidating their elemental compositions from single cells and providing information on metabolic heterogeneity in the cell population.

Metabolic engineering of microorganisms for the production of ethanol and butanol from oxides of carbon

The utilized biomass is an important consideration for sustainable biofuel production. To avoid competing with food needs, researchers have turned their attention to non-food lignocellulosic biomasses as potential feedstocks for biofuel production. However, the saccharification of a lignocellulosic biomass produces a large amount of lignin as waste. To overcome this hurdle, biomass gasification has been suggested as an alternative to saccharification. During biomass gasification, oxides of carbon (CO, CO₂) and hydrogen are produced as a major product. Accordingly, microorganisms capable of utilizing these oxides of carbon have gained attention as hosts for the production of biofuels, such as ethanol and butanol. In this work, we reviewed the Calvin cycle and Wood-Ljungdahl pathway for utilizing oxides of carbon in cyanobacteria and acetogens, respectively, and discussed the metabolic engineering strategies that may be used to produce ethanol and butanol from oxides of carbon through these routes.

Size-Segregated Chemical Compositions of HULISs in Ambient Aerosols Collected during the Winter Season in Songdo, South Korea

The primary objective of this study was to investigate the molecular compositions of humic-like substances (HULISs) in size-resolved ambient aerosols, which were collected using an Anderson-type air sampler (eight size cuts between 0.43 and 11 μm) during the winter season (i.e., the heating period of 8–12 January 2018) in Songdo, South Korea. The aerosol samples collected during the pre- (preheating, 27 November–1 December 2017) and post-winter (postheating, 12–16 March 2018) periods were used as controls for the winter season samples. According to the concentrations of the chromophoric organics determined at an ultraviolet (UV) wavelength of 305 nm, most of the HULIS compounds were found to be predominantly enriched in particles less than 2.1 μm regardless of the sampling period, which shows that particulate matter (diameter less than 2.5 μm; PM2.5) aerosols were the dominant carriers of airborne organics. Ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (UHR FT–ICR MS) analysis of the aerosol-carried organic substances revealed that as the aerosol size increased the proportions of CHO and nitrogen-containing CHO (CHON) compounds decreased, while the proportion of sulfur-containing CHO (CHOS) species increased. In particular, the ambient aerosols during the heating period seemed to present more CHO and CHON and less CHOS molecules compared to aerosols collected during the pre- and postheating periods. The aerosols collected during the heating period also exhibited more aromatic nitrogen-containing compounds, which may have originated from primary combustion processes. Overall, the particle size distribution was likely influenced by source origins; smaller particles are likely from local sources, such as traffic and industries, and larger particles (i.e., aged particles) are likely derived from long-range transport generating secondary organic aerosols (SOAs) in the atmosphere. The results of the size-segregated particles can be utilized to understand particle formation mechanisms and shed light on their toxicity to human health.

Evaluation of an untargeted nano-liquid chromatography-mass spectrometry approach to expand coverage of low molecular weight dissolved organic matter in Arctic soil

Characterizing low molecular weight (LMW) dissolved organic matter (DOM) in soils and evaluating the availability of this labile pool is critical to understanding the underlying mechanisms that control carbon storage or release across terrestrial systems. However, due to wide-ranging physicochemical diversity, characterizing this complex mixture of small molecules and how it varies across space remains an analytical challenge. Here, we evaluate an untargeted approach to detect qualitative and relative-quantitative variations in LMW DOM with depth using water extracts from a soil core from the Alaskan Arctic, a unique system that contains nearly half the Earth's terrestrial carbon and is rapidly warming due to climate change. We combined reversed-phase and hydrophilic interaction liquid chromatography, and nano-electrospray ionization coupled with high-resolution tandem mass spectrometry in positive- and negative-ionization mode. The optimized conditions were sensitive, robust, highly complementary, and enabled detection and putative annotations of a wide range of compounds (e.g. amino acids, plant/microbial metabolites, sugars, lipids, peptides). Furthermore, multivariate statistical analyses revealed subtle but consistent and significant variations with depth. Thus, this platform is useful not only for characterizing LMW DOM, but also for quantifying relative variations in LMW DOM availability across space, revealing hotspots of biogeochemical activity for further evaluation.

Structural characteristics, analytical techniques and interactions with organic contaminants of dissolved organic matter derived from crop straw: a critical review

Dissolved organic matter (DOM) represents one of the most mobile and reactive organic compounds in an ecosystem and plays an important role in the fate and transport of soil organic pollutants, nutrient cycling and more importantly global climate change. Advances in environment geochemistry in the past two decades have improved our knowledge about the genesis, composition, and structure of DOM, and its effect on the environment. Application of analytical technology, for example UV-visible spectroscopy (UV-Vis), Fourier transform infrared spectroscopy (FTIR), Nuclear magnetic resonance (NMR) spectroscopy, and three-dimensional fluorescence spectroscopy (3D-EEM) have resulted in these advances. At present, crop straw, as a part of energy development strategy, is mainly used for soil amendment, fodder, fertilizer and industrial materials. Moreover, the fermentation and decomposition of straw should be also promoted for ecological agriculture. However, few studies have focused on the structural properties of DOM derived from crop straw in farmland soil. In this article, DOM derived from crop straw, which is abbreviated to "CDOM", presents active physicochemical properties that can affect the migration and bioavailability of organic contaminants (OCs) in terrestrial ecosystems. The objectives of this review paper are: (i) to discuss the structural characteristics, analytical techniques and interactions between CDOM and OCs in farmland soil; (ii) to present a critical analysis of the impact of CDOM on the physicochemical transformation and transport of OCs in farmland soils; (iii) to provide the perspectives in future research. Therefore, the findings obtained from this study can be utilized to evaluate the relations of interactions between CDOM and OCs in agricultural soils, in order to support some suggestions for future development in agricultural waste recycling, buffering of organic pollution, and the effect on the global carbon cycle.