Soil Organic Matter Characterization by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR MS): A Critical Review of Sample Preparation, Analysis, and Data Interpretation

Challenges in quantifying and characterizing dissolved organic carbon: Sampling, isolation, storage, and analysis

Despite the advancements in analytical techniques, there are still great challenges and difficulties in accurately and effectively quantifying and characterizing dissolved organic carbon (DOC) in environmental samples. The objectives of this review paper are (a) to understand the roles and variability of DOC along the water continuum; (b) to identify the constraints, inconsistences, limitations, and artifacts in DOC characterization; and (c) to provide recommendations and remarks to improve the analytical accuracy. For the first objective, we summarize the four ecological and engineering roles of DOC along the water continuum from source water to municipal utility, including nutrients and energy sources, controlling the fates of micropollutants, buffering capacity, and treatability and precursors of disinfection byproducts. We also discuss three major challenges in DOC analysis, including spatial and temporal variations, degradability and stability, and unknown structures and formulas. For the second objective, we review the procedures and steps in DOC analysis, including sampling in diverse environmental matrices, isolation of DOC fraction, storage and preservation techniques, and analyses on bulk chemical characteristics. We list and discuss the available options and evaluate the advantages and disadvantages of each choice. Last, we provide recommendations and remarks for each stage: sampling, isolation, storage, and analysis.

Improved Dynamic Range, Resolving Power, and Sensitivity Achievable with FT-ICR Mass Spectrometry at 21 T Reveals the Hidden Complexity of Natural Organic Matter

Fourier transform ion-cyclotron resonance mass spectrometry (FT-ICR MS) is the only mass analyzer that can resolve the molecular complexity of natural organic matter at the level of elemental composition assignment. Here, we leverage the high dynamic range, resolving power, resistance to peak coalescence, and maximum ion number and ion trapping duration in a custom built, 21 tesla hybrid linear ion trap /FT-ICR mass spectrometer for a dissolved organic matter standard (Suwanne River Fulvic Acid). We compare the effect of peak-picking threshold (3σ, 4σ, 5σ, and 6σ) on number of elemental composition assignments, mass measurement accuracy, and dynamic range for a 6.3 s transient across the mass range of m/z 200-1200 that comprises the highest achieved resolving power broadband FT-ICR mass spectrum collected to date. More than 36 000 species are assigned with signal magnitude greater than 3σ at root-mean-square mass error of 36 ppb, the most species identified reported to date for dissolved organic matter. We identify ¹⁸O and ¹⁷O isotopologues and resolve isobaric overlaps on the order of a few electrons across a wide mass range (up to m/z 1000) leveraging mass resolving powers (3 000 000 at m/z 200) only achievable by 21 T FT-ICR MS and increased by ∼30% through absorption mode data processing. Elemental compositions unique to the 3σ span a wide compositional range of aromaticity not detected at higher peak-picking thresholds. Furthermore, we leverage the high dynamic range at 21 T FT-ICR MS to provide a molecular catalogue of a widely utilized reference standard (SRFA) to the analytical community collected on the highest performing mass analyzer for complex mixture analysis to date. This instrument is available free of charge to scientists worldwide.

Mass Difference Matching Unfolds Hidden Molecular Structures of Dissolved Organic Matter

Ultrahigh-resolution Fourier transform mass spectrometry (FTMS) has revealed unprecedented details of natural complex mixtures such as dissolved organic matter (DOM) on a molecular formula level, but we lack approaches to access the underlying structural complexity. We here explore the hypothesis that every DOM precursor ion is potentially linked with all emerging product ions in FTMS² experiments. The resulting mass difference (Δm) matrix is deconvoluted to isolate individual precursor ion Δm profiles and matched with structural information, which was derived from 42 Δm features from 14 in-house reference compounds and a global set of 11 477 Δm features with assigned structure specificities, using a dataset of ∼18 000 unique structures. We show that Δm matching is highly sensitive in predicting potential precursor ion identities in terms of molecular and structural composition. Additionally, the approach identified unresolved precursor ions and missing elements in molecular formula annotation (P, Cl, F). Our study provides first results on how Δm matching refines structural annotations in van Krevelen space but simultaneously demonstrates the wide overlap between potential structural classes. We show that this effect is likely driven by chemodiversity and offers an explanation for the observed ubiquitous presence of molecules in the center of the van Krevelen space. Our promising first results suggest that Δm matching can both unfold the structural information encrypted in DOM and assess the quality of FTMS-derived molecular formulas of complex mixtures in general.

Development of an Internal Calibration Algorithm for Ultrahigh-Resolution Mass Spectra of Dissolved Organic Matter

In order to obtain a spectrum with high mass accuracy, an internal calibration of Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) is inevitable. This in turn is critical for subsequent data processing and is generally performed using the commercial instrument software DataAnalysis in the benchmark calibration mode. However, no methodological study has systemically addressed the automated internal calibration of FTICR-MS spectra for dissolved organic matter (DOM) from different sources such as terrestrial and aquatic environments. In this study, a new piecewise algorithm, FTMSCalibrate, was developed to automatically calibrate FTICR-MS spectra in both positive and negative ion modes. FTMSCalibrate was found to reproduce 91.7% ± 4.4% (referred to as the true positive ratio) of the chemical formulas obtained by calibration using manual DataAnalysis. In addition to significantly reducing the mass error, FTMSCalibrate is more accurate in terms of the molecular formula assignment for low m/z peaks than Formularity and MFAssignR. FTMSCalibrate was compatible with deprotonated ions for FTICR-MS spectra in the negative ion mode as well as protonated and adduct ions, including Na- and K-adducts, for FTICR-MS spectra in the positive ion mode. These results suggest that FTMSCalibrate publicly available herein is a robust alternative for the internal calibration of FTICR-MS spectra during postdata processing and will facilitate DOM analysis by FTICR-MS.

FT-ICR/MS deciphers formation of unknown macromolecular disinfection byproducts from algal organic matters after plasma oxidation

Algal organic matter (AOM) is a potential precursor of disinfection byproducts (DBPs) in water treatment. It is a major challenge to identify macromolecular DBPs due to the diversity of AOM. In this study, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS) was applied to diagnose the AOM diversity after algae removal by plasma oxidation and to recognize the macromolecular DBPs in subsequent chlorination. Significant removal of AOM released by M. aeruginosa, C. raciborskii, and A. spiroies was achieved by plasma oxidation, accompanied by decrease in the proportion of CHNO formulas and increase in CHO formulas. Without plasma treatment, chlorination generated approximately 2486 macromolecular carbonaceous DBPs (C-DBPs) and 1984 nitrogenous DBPs (N-DBPs), with C₁₁H_nO_mCl_x and C₁₈H_nN_mO_zCl_x as the most abundant DBPs. The numbers of C-DBPs and N-DBPs decreased by 63.3% and 62.9%, respectively, if plasma treatment was applied prior to chlorination. Network computational analysis revealed that Cl substitution was the main formation pathway of AOM-derived DBP formation rather than HOCl addition. The precursors of macromolecular DBPs contained a characteristic atomic number of C and O (7 ≤ C ≤ 18; 3 ≤ O ≤ 11). This study firstly disclosed the relationship between AOM diversity and novel macromolecular DBPs during algae-laden water treatment.

Nitrogen Enrichment during Soil Organic Matter Burning and Molecular Evidence of Maillard Reactions

Wildfires in forested watersheds dramatically alter stored and labile soil organic matter (SOM) pools and the export of dissolved organic matter (DOM). Ecosystem recovery after wildfires depends on soil microbial communities and revegetation and therefore is limited by the availability of nutrients, such as nitrogen-containing and labile, water-soluble compounds. However, SOM byproducts produced at different wildfire intensities are poorly understood, leading to difficulties in assessing wildfire severity and predicting ecosystem recovery. In this work, water-extractable organic matter (WEOM) from laboratory microcosms of soil burned at discrete temperatures was characterized by ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry to study the impacts of fire temperature on SOM and DOM composition. The molecular composition derived from different burn temperatures indicated that nitrogen-containing byproducts were enriched with heating and composed of a wide range of aromatic features and oxidation states. Mass difference-based analysis also suggested that products formed during heating could be modeled using transformations along the Maillard reaction pathway. The enrichment of N-containing SOM and DOM at different soil burning intensities has important implications for ecosystem recovery and downstream water quality.

Enhanced chemodiversity, distinctive molecular signature and diurnal dynamics of dissolved organic matter in streams of two headwater catchments, Southeastern China

Dissolved organic matter (DOM) is a complicated assembly of organic molecules, including thousands of molecules with various structures and properties. However, how the stream DOM sources respond to carbon compositions and the transformation processes remains unclear. In this study, the chemical characteristics and spectral and mass spectrometry (FT-ICR MS) of DOM were analyzed. Six sampling points of headwater stream (HWSs) were sampled, and an effluent polluted stream (WSR) and a main stream of the Changjiang River (DT) were also sampled for comparison. In situ degradation experiments and FT-ICR MS analysis were also performed to observe the dynamic processes of DOM in HWS. The results showed that the anthropogenic markers of sewage (i.e. sulfur (S) compounds and marker from antibiotics and estrogen) in HWS were higher than those in DT. The molecular weight decreased while the degradation products (S-containing compounds and unsaturated compounds (HU)) increased after in situ degradation due to the influence of both the photodegradation and biodegradation process. In addition, the KMD plots showed that the DOM homologue intensities in range 400-600 Da changed significantly after demethylation by biodegradation. The components of highly refractory substances and the degradation degree of DOM in DT was higher than that in HWS. We extracted the refractory DOM pool in HWS, which was mainly small molecular with molecular weights < 600 Da. These molecular will be difficult to remove in traditional drinking water treatment processes and easily produced disinfection byproducts (DBPs). This study emphasized the necessity of identifying the sources and transformation processes of DOM in HWS and clarified the types and characteristics of DOM that should be considered in future drinking water treatment.

PFAS Analysis with Ultrahigh Resolution 21T FT-ICR MS: Suspect and Nontargeted Screening with Unrivaled Mass Resolving Power and Accuracy

Per- and polyfluoroalkyl substances (PFASs) are a large family of thousands of chemicals, many of which have been identified using nontargeted time-of-flight and Orbitrap mass spectrometry methods. Comprehensive characterization of complex PFAS mixtures is critical to assess their environmental transport, transformation, exposure, and uptake. Because 21 tesla (T) Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) offers the highest available mass resolving power and sub-ppm mass errors across a wide molecular weight range, we developed a nontargeted 21 T FT-ICR MS method to screen for PFASs in an aqueous film-forming foam (AFFF) using suspect screening, a targeted formula database (C, H, Cl, F, N, O, P, S; ≤865 Da), isotopologues, and Kendrick-analogous mass difference networks (KAMDNs). False-positive PFAS identifications in a natural organic matter (NOM) sample, which served as the negative control, suggested that a minimum length of 3 should be imposed when annotating CF₂-homologous series with positive mass defects. We putatively identified 163 known PFASs during suspect screening, as well as 134 novel PFASs during nontargeted screening, including a suspected polyethoxylated perfluoroalkane sulfonamide series. This study shows that 21 T FT-ICR MS analysis can provide unique insights into complex PFAS composition and expand our understanding of PFAS chemistries in impacted matrices.

Dynamics of organic matter molecular composition under aerobic decomposition and their response to the nitrogen addition in grassland soils

Grassland soils store a substantial proportion of the global soil carbon (C) stock. The transformation of C in grassland soils with respect to chemical composition and persistence strongly regulate the predicted terrestrial-atmosphere C flux in global C biogeochemical cycling models. In addition, increasing atmospheric nitrogen (N) deposition alters C chemistry in grassland soils. However, there remains controversy about the importance of mineralogical versus biochemical preservation of soil C, as well as uncertainty regarding how grassland soil C chemistry responds to elevated N. This study used grassland soils with diverse soil organic matter (SOM) chemistries in an 8-month aerobic incubation experiment to evaluate whether the chemical composition of SOM converged across sites over time, and how SOM persistence responded to the N addition. This study demonstrates that over the course of incubation, the richness of labile compounds decreased in soils with less ferrihydrite content, whereas labile compounds were more persistent in ferrihydrite rich soils. In contrast, we found that the richness of more complex compounds increased over the incubation in most sites, independent of soil mineralogy. Moreover, we demonstrate the extent to which the diverse chemical composition of SOM converged among sites in response to microbial decomposition. N fertilization decreased soil respiration and inhibited the convergence of molecular composition across ecosystems by altering N demand for microbial metabolism and chemical interactions between minerals and organic molecules. This study provides original evidence that the decomposition and metabolism of labile organic molecules were largely regulated by soil mineralogy (physicochemical preservation), while the metabolism of more complex organic molecules was controlled by substrate complexity (biochemical preservation) independent to mineral-organic interactions. This study advanced our understanding of the dynamic biogeochemical cycling of C by unveiling that N addition dampened C respiration and diminished the convergence of SOM chemistry across diverse grassland ecosystems.

Direct and Indirect Electron Transfer Routes of Chromium(VI) Reduction with Different Crystalline Ferric Oxyhydroxides in the Presence of Pyrogenic Carbon

Electron transfer mediated by iron minerals is considered as a critical redox step for the dynamics of pollutants in soil. Herein, we explored the reduction process of Cr(VI) with different crystalline ferric oxyhydroxides in the presence of pyrogenic carbon (biochar). Both low- and high-crystallinity ferric oxyhydroxides induced Cr(VI) immobilization mainly via the sorption process, with a limited reduction process. However, the Cr(VI) reduction immobilization was inspired by the copresence of biochar. Low-crystallinity ferric oxyhydroxide had an intense chemical combination with biochar and strong sorption for Cr(VI) via inner-sphere complexation, leading to the indirect electron transfer route for Cr(VI) reduction, that is, the electron first transferred from biochar to iron mineral through C-O-Fe binding and then to Cr(VI) with Fe(III)/Fe(II) transformation on ferric oxyhydroxides. With increasing crystallinity of ferric oxyhydroxides, the direct electron transfer between biochar and Cr(VI) became the main electron transfer avenue for Cr(VI) reduction. The indirect electron transfer was suppressed in the high-crystallinity ferric oxyhydroxides due to less sorption of Cr(VI), limited combination with biochar, and higher iron stability. This study demonstrates that electron transfer mechanisms involving iron minerals change with the mineral crystallization process, which would affect the geochemical process of contaminants with pyrogenic carbon.

Data-Based Chemical Class Regions for Van Krevelen Diagrams

Ultrahigh resolution mass spectrometry (UHR-MS) is commonly used to characterize natural organic matter (NOM). The complexity of both NOM and the data set produced make data visualization challenging. Van Krevelen diagrams─plots of component hydrogen/carbon (H/C) against oxygen/carbon (O/C) elemental ratios─have become a popular way to visualize the chemical formulas identified by UHR-MS. Different regions on the van Krevelen diagram have been attributed to different chemical classes; however, the classifications vary between studies and the regions lack standard definitions. Here, chemical formulas were obtained from public databases to create H/C and O/C ranges for amino sugar, carbohydrate, lignin, lipid, peptide, and tannin chemical classes on van Krevelen diagrams. The recommended H/C and O/C ranges are presented in a table and can be adapted to any data analysis software programs. The regions recommended here agreed reasonably well with previous literature for amino sugar, carbohydrate, lignin, lipid, and peptide regions. However, the recommended tannin region appears at lower H/C ratio values and with a wider range of O/C ratio values compared to previous studies. The regions presented herein are strongly recommended for use as consistent reference points in future NOM characterization studies to aid in the discussion of data and to readily compare studies.

High-Resolution Molecular-Level Characterization of a Blanket Bog Peat Profile

To understand peatland carbon-cycling processes ultimately requires the ability to track changes occurring on the molecular-level. In this study, we profile a peat core taken from the world's largest blanket bog, Flow Country, Scotland, using physicochemical properties, ATR-FTIR, solid/liquid-state NMR, and solid/liquid-state FT-ICR-MS. Air-dried peat and labile and recalcitrant peat extracts, including pore water dissolved organic matter (PW-DOM), are analyzed and the merits of each technique are discussed. Solid-state NMR demonstrated changing distribution of compound classes with core depth and water table, the latter not picked up by IR. Liquid-state NMR and MS both demonstrated variations in molecular composition along the core depth in all phases and extracts. Contrary to previous reports, the composition of PW-DOM varied with depth. Major compounds, some previously unreported, identified by 1D/2D NMR occurred throughout the core, suggesting the existence of hot spots of microbial activity/compound accumulation. Offering complementary views, the techniques provided evidence of gradual molecular level changes with age, zonation due to the water table, and hot spots due to microbial activity. This study provides new insights into the molecular signatures of peat layers and establishes the foundation for examining peat function and health at the molecular-level.

Chemodiversity of Dissolved Organic Matter and Its Molecular Changes Driven by Rhizosphere Activities in Fe Ore Tailings Undergoing Eco-Engineered Pedogenesis

Dissolved organic matter (DOM) plays an important role in soil structure and biogeochemical function development, which are fundamental for the eco-engineering of tailings-soil formation to underpin sustainable tailings rehabilitation. In the present study, we have characterized the DOM composition and its molecular changes in an alkaline Fe ore tailing primed with organic matter (OM) amendment and plant colonization. The results demonstrated that microbial OM decomposition dramatically increased DOM richness and average molecular weight, as well as its degree of unsaturation, aromaticity, and oxidation in the tailings. Plant colonization drove molecular shifts of DOM by depleting the unsaturated compounds with a high value of nominal oxidation state of carbon (NOSC), such as tannin-like and carboxyl-rich polycyclic-like compounds. This may be partially related to their sequestration by secondary Fe-Si minerals formed from rhizosphere-driven mineral weathering. Furthermore, the molecular shifts of DOM may have also resulted from plant-regulated microbial community changes, which further influenced DOM molecules through microbial-DOM interactions. These findings contribute to the understanding of DOM biogeochemistry and ecofunctionality in the tailings during early pedogenesis driven by OM input and pioneer plant/microbial colonization, providing an important basis for the development of strategies and technologies toward the eco-engineering of tailings-soil formation.