A History of Molecular Level Analysis of Natural Organic Matter by FTICR Mass Spectrometry and The Paradigm Shift in Organic Geochemistry

Selective molecular characterization of organic aerosols using in situ laser desorption ionization mass spectrometry

RATIONALE

The sources and chemical compositions of organic aerosol (OA) exert a significant influence on both regional and global atmospheric conditions, thereby having far-reaching implications on environmental chemistry. However, existing mass spectrometry (MS) methods have limitations in characterizing the detailed composition of OA due to selective ionization as well as fractionation during cold-water extraction and solid-phase extraction (SPE).

METHODS

A comprehensive MS study was conducted using aerosol samples collected on dusty, clean, and polluted days. To supplement the data obtained from electrospray ionization (ESI), a strategy for analyzing OAs collected using the quartz fiber filter directly utilizing laser desorption ionization (LDI) was employed. Additionally, the ESI method was conducted to explore suitable approaches for determining various OA compositions from samples collected on dusty, clean, and polluted days.

RESULTS

In situ LDI has the advantages of significantly reducing the sample volume, simplifying sample preparation, and overcoming the problem of overestimating sulfur-containing compounds usually encountered in ESI. It is suitable for the characterization of highly unsaturated and hydrophobic aerosols, such as brown carbon-type compounds with low volatility and high stability, which is supplementary to ESI.

CONCLUSIONS

Compared with other ionization methods, in situ LDI helps provide a complementary description of the molecular compositions of OAs, especially for analyzing OAs in polluted day samples. This method may contribute to a more comprehensive MS analysis of the elusive compositions and sources of OA in the atmosphere.

Critical review of fluorescence and absorbance measurements as surrogates for the molecular weight and aromaticity of dissolved organic matter

Dissolved organic matter (DOM) is ubiquitous in aquatic environments and challenging to characterize due to its heterogeneity. Optical measurements (i.e., absorbance and fluorescence spectroscopy) are popular characterization tools, because they are non-destructive, require small sample volumes, and are relatively inexpensive and more accessible compared to other techniques (e.g., high resolution mass spectrometry). To make inferences about DOM chemistry, optical surrogates have been derived from absorbance and fluorescence spectra to describe differences in spectral shape (e.g., E2:E3 ratio, spectral slope, fluorescence indices) or quantify carbon-normalized optical responses (e.g., specific absorbance (SUVA) or specific fluorescence intensity (SFI)). The most common interpretations relate these optical surrogates to DOM molecular weight or aromaticity. This critical review traces the genesis of each of these interpretations and, to the extent possible, discusses additional lines of evidence that have been developed since their inception using datasets comparing diverse DOM sources or strategic endmembers. This review draws several conclusions. More caution is needed to avoid presenting surrogates as specific to either molecular weight or aromaticity, as these physicochemical characteristics are often correlated or interdependent. Many surrogates are proposed using narrow contexts, such as fractionation of a limited number of samples or dependence on isolates. Further study is needed to determine if interpretations are generalizable to whole-waters. Lastly, there is a broad opportunity to identify why endmembers with low abundance of aromatic carbon (e.g., effluent organic matter, Antarctic lakes) often do not follow systematic trends with molecular weight or aromaticity as observed in endmembers from terrestrial environments with higher plant inputs.

MS and NMR Analysis of Isotopically Labeled Chloramination Disinfection Byproducts: Hyperlinks and Chemical Reactions

FT-ICR MS and NMR analysis of an isotopically labeled complex mixture of water disinfection byproducts formed by chloramine disinfection of model phenolic acids is described. A new molecular formula assignment procedure using the CoreMS Python library able to assign isotopically enriched formulas is proposed. Statistical analysis of the assigned formulas showed that the number of compounds, the diversity of the mixture, and the chlorine count increase during the chloramination reaction. The complex reaction mixture was investigated as a network of reactions using PageRank and Reverse PageRank algorithms. Independent of the MS signal intensities, the PageRank algorithm calculates the formulas with the highest probability at convergence of the reaction; these were chlorinated and nitrated derivatives of the starting materials. The Reverse PageRank revealed that the most probable chemical transformations in the complex mixture were chlorination and decarboxylation. These agree with the data obtained from INADEQUATE NMR spectra and literature data, indicating that this approach could be applied to gain insight into reactions pathways taking place in complex mixtures without any prior knowledge.

Seasonal variation and dissolved organic matter influence on the distribution, transformation, and environmental risk of pharmaceuticals and personal care products in coastal zone: A case study of Tianjin, China

Pharmaceuticals and personal care products (PPCPs) are emerging contaminants that have raised urgent environmental issues. The dissolved organic matter (DOM) plays a pivotal role on PPCPs' migration and transformation. To obtain a comprehensive understanding of the occurrence and distribution of PPCPs, a seasonal sampling focused on the riverine system in coastal zone, Tianjin, Bohai Rim was conducted. The distribution and transformation of thirty-three PPCPs and their interaction with DOM were investigated, and their sources and ecological risks were further evaluated. The total concentration of PPCPs ranges from 0.01 to 197.20 μg/L, and such value is affected by regional temperature, DOM and land use types. PPCPs migration at soil-water interface is controlled by temperature, sunlight, water flow and DOM. PPCPs have a high affinity to the protein-like DOM, while the humus-like DOM plays a negative influence and facilitates PPCPs' degradation. It is also found that protein-like DOM can represent point source pollution, while humus-like substances indicate non-point source (NPS) emission. Specific PPCPs can be used as markers to trace the source of domestic discharge. Additionally, daily use PPCPs such as ketoprofen, caffeine and iopromide are estimated to be the main risk substances, and their ecological risk varies on space, season and river hydraulic condition.

Phototransformation of Brominated Disinfection Byproducts and Toxicity Elimination in Sunlit-Ozonated Reclaimed Water

Ozonation is universally used during water treatment but can form hazardous brominated disinfection byproducts (Br-DBPs). While sunlight exposure is advised to reduce the risk of Br-DBPs, their phototransformation pathways remain insufficiently understood. Here, sunlight irradiation was found to reduce adsorbable organic bromine by 63%. Applying high-resolution mass spectrometry, the study investigated transformations of dissolved organic matter in sunlit-ozonated reclaimed water, revealing the number and abundance of assigned formulas decreased after irradiation. The Br-DBPs with O/C < 0.6 and MW > 400 Da were decreased or removed after irradiation, with the majority being CHOBr compounds. The peak intensity reduction ratio of CHOBr compounds correlated positively with double bound equivalent minus oxygen ratios but negatively with O/C, suggesting that photo-susceptible CHOBr compounds were highly unsaturated. Mass difference analysis revealed that the photodegradation pathways were mainly oxidation aligned with debromination. Three typical CHOBr molecular structures were resolved, and their photoproducts were proposed. Toxicity estimates indicated decreased toxicity in these photoproducts compared to their parent compounds, in line with experimentally determined values. Our proposed phototransformation pathways for Br-DBPs enhance our comprehension of their degradation and irradiation-induced toxicity reduction in reclaimed water, further illuminating their transformation under sunlight in widespread environmental scenarios.

Characterization of halogenated organic compounds by the Fourier transform ion cyclotron resonance mass spectrometry: A critical review

Halogenated organic compounds (HOCs), widely present in various environments, are generally formed by natural processes (e.g., photochemical halogenation) and anthropogenic activities (e.g., water disinfection and anthropogenic discharge of HOCs), posing health and environmental risks. Therefore, in-depth knowledge of the molecular composition, transformation, and fate of HOCs is crucial to regulate and reduce their formation. Because of the extremely complex nature of HOCs and their precursors, the molecular composition of HOCs remains largely unknown. The Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) offers the most powerful resolution and mass accuracy for the simultaneous molecular-level characterization of HOCs and their precursors. However, there is still a paucity of reviews regarding the comprehensive characterization of HOCs by FT-ICR MS. Based on the FT-ICR MS, the formation mechanism, sample pretreatment, and analysis methods were summarized for two typical HOCs classes, namely halogenated disinfection byproducts and per- and polyfluoroalkyl substances in this review. Moreover, we have highlighted data analysis methods and some typical applications of HOCs using FT-ICR MS and proposed suggestions for current issues. This review will deepen our understanding of the chemical characterization of HOCs and their formation mechanisms and transformation at the molecular level in aquatic systems, facilitating the application of the state-of-the-art FT-ICR MS in environmental and geochemical research.

Quantifying Stochastic Processes in Shaping Dissolved Organic Matter Pool with High-Resolution Mass Spectrometry

Natural dissolved organic matter (DOM) represents a ubiquitous molecular mixture, progressively characterized by spatiotemporal resolution. However, an inadequate comprehension of DOM molecular dynamics, especially the stochastic processes involved, hinders carbon cycling predictions. This study employs ecological principles to introduce a neutral theory to elucidate the fundamental processes involving molecular generation, degradation, and migration. A neutral model is thus formulated to assess the probability distribution of DOM molecules, whose frequencies and abundances follow a β-distribution relationship. The neutral model is subsequently validated with high-resolution mass spectrometry (HRMS) data from various waterbodies, including lakes, rivers, and seas. The model fitting highlights the prevalence of molecular neutral distribution and quantifies the stochasticity within DOM molecular dynamics. Furthermore, the model identifies deviations of HRMS observations from neutral expectations in photochemical and microbial experiments, revealing nonrandom molecular transformations. The ecological null model further validates the neutral modeling results, demonstrating that photodegradation reduces molecular stochastic dynamics at the surface of an acidic pit lake, while random distribution intensifies at the river surface compared with the porewater. Taken together, the DOM molecular neutral model emphasizes the significance of stochastic processes in shaping a natural DOM pool, offering a potential theoretical framework for DOM molecular dynamics in aquatic and other ecosystems.

Selectivity of β-Cyclodextrin Polymer toward Aquatic Contaminants: Insights from Ultrahigh-Resolution Mass Spectrometry of Dissolved Organic Matter

Selectivity in solid-phase extraction (SPE) materials has become increasingly important for analyte enrichment in sensitive analytical workflows to alleviate detrimental matrix effects. Molecular-level investigation of matrix constituents, which are preferentially extracted or excluded, can provide the analytical chemist with valuable information to learn about their control on sorbent selectivity. In this work, we employ nontargeted Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) to elucidate the molecular chemodiversity of freshwater-derived dissolved organic matter (DOM) extracted by the selective model sorbent β-cyclodextrin polymer (β-CDP) in comparison to conventional, universal SPE sorbents (i.e., Oasis HLB, Supel-Select HLB, and LiChrolut EN). Statistical analysis of MS data corroborated the highly selective nature of β-CDP by revealing the extracted DOM spectra that are most dissimilar to original compositions. We found that its selectivity was characterized by pronounced discrimination against highly oxygenated and unsaturated DOM compounds, which were associated with the classes of lignin-like, tannin-like, and carboxylic-rich alicyclic molecules. In contrast, conventional sorbents excluded less highly oxygenated compounds and showed a more universal extraction behavior for a wide range of DOM compositional space. We lay these findings in a larger context that aids the analyst in obtaining an a priori estimate of sorbent selectivity toward any target analyte of interest serving thereby an optimization of sample preparation. This study highlights the great value of nontargeted ultrahigh-resolution MS for better understanding of targeted analytics and provides new insights into the selective sorption behavior of novel sorbents.

Molecular composition of dissolved organic matter across diverse ecosystems: Preliminary implications for biogeochemical cycling

Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) has been widely applied to characterize the molecular composition of dissolved organic matter (DOM) in different ecosystems. Most previous studies have explored the molecular composition of DOM focused on one or a few ecosystems, which prevents us from tracing the molecular composition of DOM from different sources and further exploring its biogeochemical cycling across ecosystems. In this study, a total of 67 DOM samples, including soil, lake, river, ocean, and groundwater, were analyzed by negative-ion electrospray ionization FT-ICR MS. Results show that molecular composition of DOM varies dramatically among diverse ecosystems. Specifically, the forest soil DOM exhibited the strongest terrestrial signature of molecules, while the seawater DOM showed the most abundant of biologically recalcitrant components, for example, the carboxyl-rich alicyclic molecules were abundant in the deep-sea waters. Terrigenous organic matter is gradually degraded during its transport along the river-estuary-ocean continuum. The saline lake DOM showed similar DOM characteristics with marine DOM, and sequestrated abundant recalcitrant DOM. By comparing these DOM extracts, we found that human activities likely lead to an increase in the content of S and N-containing heteroatoms in DOM, this phenomenon was commonly found in the paddy soil, polluted river, eutrophic lake, and acid mine drainage DOM samples. Overall, this study compared molecular composition of DOM extracted from various ecosystems, providing a preliminary comparison on the DOM fingerprint and an angle of view into biogeochemical cycling across different ecosystems. We thus advocate for the development of a comprehensive molecular fingerprint database of DOM using FT-ICR MS across a wider range of ecosystems. This will enable us to better understand the generalizability of the distinct features among ecosystems.

Discriminative Behavior of Cyclodextrin Polymers against Dissolved Organic Matter: Role of Cavity Size and Sorbate Properties

Cyclodextrin polymers (CDPs) are promising next-generation adsorbents in water purification technologies. The selectivity of the polymer derivate cross-linked with tetrafluoroterephthalonitrile (TFN-CDP) for nonionic and cationic micropollutants (MPs) over dissolved organic matter (DOM) renders the adsorbent also attractive for many analytical applications. The molecular drivers of the observed selectivity are, nonetheless, not yet fully understood. To provide new insights into the sorption mechanism, we (i) synthesized TFN-CDPs with different cavity sizes (α-, β-, γ-CDP); (ii) assessed their extraction efficiencies for selected nonionic MPs in competition with different DOM size fractions (<1, 1-3, 3-10, >10 kDa) to test for size-selectivity; and (iii) performed nontargeted, ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry analysis on CDP-extracted DOM compounds (<1 kDa) to probe for molecular sorbate properties governing their selective sorption. First, no evidence of size-selectivity was obtained through either the different CD cavity sizes (i) or the two independent approaches (ii) and (iii). Second, we found a dominant impact of sorbate oxygenation and polarity on the extraction of DOM and MPs, respectively, with relatively oxygen-poor/nonpolar molecules favorably retained on all α-, β-, and γ-CDP. Third, our data indicates exclusion of an anionic matrix, such as carboxylic acids, but preferential sorption of cationic nitrogen-bearing DOM, pointing at repulsive and attractive forces with the negatively charged cross-linker as a likely reason. Therefore, we ascribe TFN-CDP's selectivity to nonpolar and electrostatic interactions between MPs/DOM and the polymer building blocks. These molecular insights can further aid in the optimization of efficient and selective sorbent design for environmental and analytical applications.

Ecotoxicological significance of bio-corona formation on micro/nanoplastics in aquatic organisms

The unsustainable manufacturing, utilization and inadequate handling of plastics have led to a surge in global plastic pollution. In recent times, there has been increasing concern about the plausible hazards associated with exposure to micro/nanoplastics (M/NPs). As aquatic systems are considered to be the likely sink for M/NPs, it is crucial to comprehend their environmental behavior. The bioavailability, toxicity and fate of M/NPs in the environment are predominantly dictated by their surface characteristics. In the aquatic environment, M/NPs are prone to be internalized by aquatic organisms. This may facilitate their interaction with a diverse array of biomolecules within the organism, resulting in the formation of a biocorona (BC). The development of BC causes modifications in the physicochemical attributes of the M/NPs including changes to their size, stability, surface charge and other properties. This review details the concept of BC formation and its underlying mechanism. It provides insight on the analytical techniques employed for characterizing BC formation and addresses the associated challenges. Further, the eco-toxicological implications of M/NPs and the role of BC in modifying their potential toxicity on aquatic organisms is specified. The impact of BC formation on the fate and transport of M/NPs is discussed. A concise outlook on the future perspectives is also presented.

MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data

BACKGROUND

Microbiomes are now recognized as the main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e., metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking.

RESULTS

Here, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line-based pipeline for the analysis (e.g., chemodiversity analysis, multivariate statistics), visualization (e.g., Van Krevelen diagrams, elemental and molecular class composition plots), and presentation of direct injection high-resolution FT-ICR MS data sets after molecular formula assignment has been performed. When compared to other available FT-ICR MS software, MetaboDirect is superior in that it requires a single line of code to launch a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is also uniquely able to automatically generate biochemical transformation networks (ab initio) based on mass differences (mass difference network-based approach) that provide an experimental assessment of metabolite connections within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses.

CONCLUSION

Application of MetaboDirect to FT-ICR MS-based metabolomic data sets from a marine phage-bacterial infection experiment and a Sphagnum leachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. The source code and User's guide of MetaboDirect are freely available through ( https://github.com/Coayala/MetaboDirect ) and ( https://metabodirect.readthedocs.io/en/latest/ ), respectively. Video Abstract.

Effect of fire on characteristics of dissolved organic matter in forested catchments in the Mediterranean biome: A review

Fires in forested catchments pose a water contamination risk from fire-derived dissolved organic matter (DOM). Fire events are expected to increase under a projection of warmer and drier climatic conditions; therefore, understanding the consequences of fire-derived DOM is critical for water supply and management of drinking water and catchments. This paper addresses how fire regime - the intensity, severity and frequency of fires - influences DOM quantity and composition in surface waters in forested catchments, and how long it takes for water quality to recover to pre-fire levels. A review of post-fire studies in Mediterranean regions reporting on DOM related parameters has been conducted. The literature shows that post-fire DOM composition and reactivity is different from DOM generated under processes of biological degradation, and hence our reliance on DOM 'bulk properties' and surrogate DOM bulk parameters may not provide sufficient information to deal with the potential complexity of the organic compounds produced by a catchment fire. Appropriate measures are important to adequately operate conventional water treatment facilities, for example. Critical parameters for the effects of burning include the alteration of DOM composition, aromaticity, and the relative amounts of labile/recalcitrant organic components. The literature shows mixed information for the influence of both burn severity and fire intensity, on these parameters, which indicates DOM response to fire is highly variable. For fire frequency, the evidence is more unequivocal, indicating that frequent fires change the composition of DOM to components that are less bioavailable, and elevate the degree of aromaticity, which may be detrimental to water quality. In addition, and in general terms, the more recent the fire, the more aromatic and humified DOM components are found, and vice versa. The recovery of surface water quality to pre-fire conditions was variable, with no safe temporal thresholds suggested in the literature. In some cases, fire-induced changes in DOM composition were observable up to 16 years post-fire. The lack of clearly observed trends in post-fire DOM with fire regimes could be attributed to numerous factors such as limited long-term and event-based observations, experimental design challenges, and site-specific biological, physical and hydrological factors. The application of terminologies used to describe fire regimes such as burn severity and fire intensity also creates challenges in comparing the outcomes and results from numerous studies.

Description of Dissolved Organic Matter Transformational Networks at the Molecular Level

Dissolved Organic Matter (DOM) is an important component of the global carbon cycle. Unscrambling the structural footprint of DOM is key to understand its biogeochemical transformations at the mechanistic level. Although numerous studies have improved our knowledge of DOM chemical makeup, its three-dimensional picture remains largely unrevealed. In this work, we compare four solid phase extracted (SPE) DOM samples from three different freshwater ecosystems using high resolution mobility and ultrahigh-resolution Fourier transform ion cyclotron resonance tandem mass spectrometry (FT-ICR MS/MS). Structural families were identified based on neutral losses at the level of nominal mass using continuous accumulation of selected ions-collision induced dissociation (CASI-CID)FT-ICR MS/MS. Comparison of the structural families indicated dissimilarities in the structural footprint of this sample set. The structural family representation using Cytoscape software revealed characteristic clustering patterns among the DOM samples, thus confirming clear differences at the structural level (Only 10% is common across the four samples.). The analysis at the level of neutral loss-based functionalities suggests that hydration and carboxylation are ubiquitous transformational processes across the three ecosystems. In contrast, transformation mechanisms involving methoxy moieties may be constrained in estuarine systems due to extensive upstream lignin biodegradation. The inclusion of the isomeric content (mobility measurements at the level of chemical formula) in the structural family description suggests that additional transformation pathways and/or source variations are possible and account for the dissimilarities observed. While the structural character of more and diverse types of DOM samples needs to be assessed and added to this database, the results presented here demonstrate that Graph-DOM is a powerful tool capable of providing novel information on the DOM chemical footprint, based on structural interconnections of precursor molecules generated by fragmentation pathways and collisional cross sections.

Comprehensive understanding of DOM reactivity in anaerobic fermentation of persulfate-pretreated sewage sludge via FT-ICR mass spectrometry and reactomics analysis

Understanding the composition and reactivity of dissolved organic matter (DOM) at molecular level is vital for deciphering potential regulators or indicators relating to anaerobic process performance, though it was hardly achieved by traditional analyses. Here, the DOM composition, molecular reactivity and transformation in the enhanced sludge fermentation process were comprehensively elucidated using high-resolution mass spectrometry measurement, and data mining with machine learning and paired mass distance (PMD)-based reactomics. In the fermentation process for dewatered sludge, persulfate (PDS) pretreatment presented its highest performance in improving volatile fatty acids (VFAs) production with the increase from 2,711 mg/L to 3,869 mg/L, whereas its activation in the presence of Fe (as well as the hybrid of Fe and activated carbon) led to the decreased VFAs production performance. In addition to the conventional view of improved decomposition and solubilization of N-containing structures from sludge under the sole PDS pretreatment, the improved VFAs production was associated with the alternation of DOM molecular compositions such as humification generating molecules with high O/C, N/C, S/C and aromatic index (AI_mod). Machine learning was capable of predicting the DOM reactivity classes with 74-76 % accuracy and found that these molecular parameters in addition to nominal oxidation state of carbon (NOSC) were among the most important variables determining the generation or disappearance of bio-resistant molecules in the PDS pretreatment. The constructed PMD-based network suggested that highly connected molecular network with long path length and high diameter was in favor of VFAs production. Especially, -NH related transformation was found to be active under the enhanced fermentation process. Moreover, network topology analysis revealed that CHONS compounds (e.g., C₁₃H₂₇O₈N₁S₁) can be the keystone molecules, suggesting that the presence of sulfur related molecules (e.g., cysteine-like compounds) should be paid more attention as potential regulators or indicators for controlling sludge fermentation performance. This study also proposed the non-targeted DOM molecular analysis and downstream data mining for extending our understanding of DOM transformation at molecular level.

Unified Modeling Approach for Quantifying the Proton and Metal Binding Ability of Soil Dissolved Organic Matter

Soil dissolved organic matter (DOM) is composed of a mass of complex organic compounds in soil solutions and significantly affects a range of (bio)geochemical processes in soil environment. However, how the chemical complexity (i.e., heterogeneity and chemodiversity) of soil DOM molecules affects their proton and metal binding ability remains unclear, which limits our ability for predicting the environmental behavior of DOM and metals. In this study, we developed a unified modeling approach for quantifying the proton and metal binding ability of soil DOM based on Cu titration experiments, Fourier transform ion cyclotron resonance mass spectrometry data, and molecular modeling method. Although soil DOM samples from different regions have enormously heterogeneous and diverse properties, we found that the molecules of soil DOM can be divided into three representative groups according to their Cu binding capacity. Based on the molecular models for individual molecular groups and the relative contributions of each group in each soil DOM, we were able to further develop molecular models for all soil DOM to predict their molecular properties and proton and metal binding ability. Our results will help to develop mechanistic models for predicting the reactivity of soil DOM from various sources.

Characterizing Natural Organic Matter Transformations by Microbial Communities in Terrestrial Subsurface Ecosystems: A Critical Review of Analytical Techniques and Challenges

Determining the mechanisms, traits, and pathways that regulate microbial transformation of natural organic matter (NOM) is critical to informing our understanding of the microbial impacts on the global carbon cycle. The capillary fringe of subsurface soils is a highly dynamic environment that remains poorly understood. Characterization of organo-mineral chemistry combined with a nuanced understanding of microbial community composition and function is necessary to understand microbial impacts on NOM speciation in the capillary fringe. We present a critical review of the popular analytical and omics techniques used for characterizing complex carbon transformation by microbial communities and focus on how complementary information obtained from the different techniques enable us to connect chemical signatures with microbial genes and pathways. This holistic approach offers a way forward for the comprehensive characterization of the formation, transformation, and mineralization of terrestrial NOM as influenced by microbial communities.

Unsupervised Structural Classification of Dissolved Organic Matter Based on Fragmentation Pathways

Dissolved organic matter (DOM) is considered an essential component of the Earth's ecological and biogeochemical processes. Structural information of DOM components at the molecular level remains one of the most extraordinary analytical challenges. Advances in determination of chemical formulas from the molecular studies of DOM have provided limited indications on structural signatures and potential reaction pathways. In this work, we extend the structural characterization of a wetland DOM sample using precursor and fragment molecular ions obtained by a sequential electrospray ionization-Fourier transform-ion cyclotron resonance tandem mass spectrometry (ESI-FT-ICR CASI-CID MS/MS) approach. The DOM chemical complexity resulted in near 900 precursors (P) and 24 000 fragment (F) molecular ions over a small m/z 261-477 range. The DOM structural content was dissected into families of structurally connected precursors based on neutral mass loss patterns (Pn-1 + F1:n + C) across the two-dimensional (2D) MS/MS space. This workflow identified over 1900 structural families of DOM compounds based on a precursor and neutral loss (H2O, CH4O, and CO2). The inspection of structural families showed a high degree of isomeric content (numerous identical fragmentation pathways), not discriminable with sole precursor ion analysis. The connectivity map of structural families allows for the visualization of potential biogeochemical processes that DOM undergoes throughout its lifetime. This study illustrates that integrating effective computational tools on a comprehensive high-resolution mass fragmentation strategy further enables the DOM structural characterization.

Formula Assignment Algorithm for Deuterium-Labeled Ultrahigh-Resolution Mass Spectrometry: Implications of the Formation Mechanism of Halogenated Disinfection Byproducts

Ultrahigh-resolution mass spectrometry (UHR-MS) coupled with isotope labeling has attracted significant attention in elucidating the mechanisms of the transformation of dissolved organic matter (DOM). Herein, we developed a novel formula assignment algorithm based on deuterium (D)-labeled UHR-MS, namely, FTMSDeu, for the first time. This algorithm was employed to determine the precursor molecules of halogenated disinfection byproducts (X_n-DBPs) and to evaluate the relative contribution of electrophilic addition and substitution reactions in X_n-DBP formation according to the H/D exchange of DOM molecules. Further, tandem mass spectrometry with homologous-based network analysis was used to validate the formula assignment accuracy of FTMSDeu in the identification of iodinated disinfection byproducts. Electrophilic substitution accounted for 82-98, 71-89, and 43-45% of the formation for Cl-, Br-, and I-containing X_n-DBPs, respectively, indicating the dominant role of the electrophilic substitution in chlorinated disinfection byproducts with low Br and I concentrations. The absence of putative precursors in some X_n-DBPs also suggests that X_n-DBP formation includes secondary reactions (e.g., oxidation and hydrolysis) in addition to the electrophilic addition and/or substitution of halogens. These findings highlight the significance of isotopically labeled UHR-MS techniques in revealing the transformation of DOM in natural and engineered systems.

Ionization selectivity of electrospray and atmospheric pressure photoionization FT-ICR MS for petroleum refinery wastewater dissolved organic matter

Dissolved organic matter (DOM) in petroleum refinery wastewater is an extremely complex mixture. A better understanding of chemical compositions of DOM at the molecular level is necessary for the design and optimization of wastewater treatment processes. In this study, two largely different DOM samples, one from a petroleum refinery wastewater and the other from the Suwannee river water, were characterized by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) coupled with positive-/negative-ion electrospray ionization (ESI), and positive-ion atmospheric pressure photoionization (APPI). For wastewater DOM, a total of 6226 molecular formulae were assigned in the three ionization modes. However, only 1182 molecular formulae were common in all three mass spectra, indicating that the techniques were highly complementary in the types of molecules they ionize. Acid O_x (x = 1-9) and basic N₁O_x (x = 0-2) classes were dominant in the wastewater DOM detected in negative-ion and positive-ion ESI mode, respectively. And the wastewater DOM contains considerable amounts of polycyclic aromatic hydrocarbons that did not respond to ESI but can be ionized selectively by APPI. Compared with riverine DOM, the refinery wastewater DOM has a higher molecular complexity and is more enriched in hydrocarbon, and nitrogen- and sulfur-containing compounds. The results show that the major components of refinery wastewater DOM were distinctive from those of the natural organic matter. Though not quantitative, the results obtained by various ionization techniques were found to be complementary, and are helpful to our understanding of the selectivity of different ionization techniques as well as the molecular compositions of DOM.

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.

PyKrev: A Python Library for the Analysis of Complex Mixture FT-MS Data

In this paper, we present PyKrev, a Python library for the analysis of complex mixture Fourier transform mass spectrometry (FT-MS) data. PyKrev is a comprehensive suite of tools for analysis and visualization of FT-MS data after formula assignment has been performed. These comprise formula manipulation and calculation of chemical properties, intersection analysis between multiple lists of formulas, calculation of chemical diversity, assignment of compound classes to formulas, multivariate analysis, and a variety of visualization tools producing van Krevelen diagrams, class histograms, PCA score, and loading plots, biplots, scree plots, and UpSet plots. The library is showcased through analysis of hot water green tea extracts and Scotch whisky FT-ion cyclotron resonance-MS data sets. PyKrev addresses the lack of a single, cohesive toolset for researchers to perform FT-MS analysis in the Python programming environment encompassing the most recent data analysis techniques used in the field.