Moving beyond the van Krevelen Diagram: A New Stoichiometric Approach for Compound Classification in Organisms

Green fractionation and hydrolysis of fish meal to improve their techno-functional properties

A green strategy employing water as solvent has been adopted to obtain protein hydrolysates from fish meal (FM), its water-soluble fraction (WSP), and its non-water-soluble fraction (NSP). The techno-functional properties of the hydrolysates have been investigated and compared to hydrolysates obtained with Alcalase®. In general, SWH hydrolysates presented higher content of free amino acids and higher degree of hydrolysis, which reflected on the molecular size distribution. However, Alcalase® hydrolysates presented better solubility (from 74 ± 4% for NSP at pH = 2 up to 99 ± 1% for WSP at pH = 4-7). According to fluorescence experiments, FM and NSP hydrolysates showed the highest surface hydrophobicity, which has been related to better emulsifying properties and higher emulsion stability. The emulsions stabilized with 2%wt. of SWH-treated NSP showed the smallest particle sizes, with D[4,3] = 155 nm at day 0, and good stability, with D[4,3] = 220 nm at day 7, proving that water fractionation followed by SWH treatment is a good method to improve the techno-functional properties of the hydrolysates.

Bioenergetic mapping of 'healthy microbiomes' via compound processing potential imprinted in gut and soil metagenomes

Despite mounting evidence of their importance in human health and ecosystem functioning, the definition and measurement of 'healthy microbiomes' remain unclear. More advanced knowledge exists on health associations for compounds used or produced by microbes. Environmental microbiome exposures (especially via soils) also help shape, and may supplement, the functional capacity of human microbiomes. Given the synchronous interaction between microbes, their feedstocks, and micro-environments, with functional genes facilitating chemical transformations, our objective was to examine microbiomes in terms of their capacity to process compounds relevant to human health. Here we integrate functional genomics and biochemistry frameworks to derive new quantitative measures of in silico potential for human gut and environmental soil metagenomes to process a panel of major compound classes (e.g., lipids, carbohydrates) and selected biomolecules (e.g., vitamins, short-chain fatty acids) linked to human health. Metagenome functional potential profile data were translated into a universal compound mapping 'landscape' based on bioenergetic van Krevelen mapping of function-level meta-compounds and corresponding functional relative abundances, reflecting imprinted genetic capacity of microbiomes to metabolize an array of different compounds. We show that measures of 'compound processing potential' associated with human health and disease (examining atherosclerotic cardiovascular disease, colorectal cancer, type 2 diabetes and anxious-depressive behavior case studies), and displayed seemingly predictable shifts along gradients of ecological disturbance in plant-soil ecosystems (three case studies). Ecosystem quality explained 60-92 % of variation in soil metagenome compound processing potential measures in a post-mining restoration case study dataset. With growing knowledge of the varying proficiency of environmental microbiota to process human health associated compounds, we might design environmental interventions or nature prescriptions to modulate our exposures, thereby advancing microbiota-oriented approaches to human health. Compound processing potential offers a simplified, integrative approach for applying metagenomics in ongoing efforts to understand and quantify the role of microbiota in environmental- and human-health.

Improved Characterization of Soil Organic Matter by Integrating FT-ICR MS, Liquid Chromatography Tandem Mass Spectrometry, and Molecular Networking: A Case Study of Root Litter Decay under Drought Conditions

Understanding of how soil organic matter (SOM) chemistry is altered in a changing climate has advanced considerably; however, most SOM components remain unidentified, impeding the ability to characterize a major fraction of organic matter and predict what types of molecules, and from which sources, will persist in soil. We present a novel approach to better characterize SOM extracts by integrating information from three types of analyses, and we deploy this method to characterize decaying root-detritus soil microcosms subjected to either drought or normal conditions. To observe broad differences in composition, we employed direct infusion Fourier-transform ion cyclotron resonance mass spectrometry (DI-FT-ICR MS). We complemented this with liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify components by library matching. Since libraries contain only a small fraction of SOM components, we also used fragment spectral cosine similarity scores to relate unknowns and library matches through molecular networks. This integrated approach allowed us to corroborate DI-FT-ICR MS molecular formulas using library matches, which included fungal metabolites and related polyphenolic compounds. We also inferred structures of unknowns from molecular networks and improved LC-MS/MS annotation rates from ∼5 to 35% by considering DI-FT-ICR MS molecular formula assignments. Under drought conditions, we found greater relative amounts of lignin-like vs condensed aromatic polyphenol formulas and lower average nominal oxidation state of carbon, suggesting reduced decomposition of SOM and/or microbes under stress. Our integrated approach provides a framework for enhanced annotation of SOM components that is more comprehensive than performing individual data analyses in parallel.

Effect of surface functional groups of polystyrene micro/nano plastics on the release of NOM from flocs during the aging process

Currently, the hidden risk of microplastics in the coagulation process has attracted much attention. However, previous studies aimed at improving the removal efficiency of microplastics and ignored the importance of interactions between microplastics and natural organic matter (NOM). This study investigated how polystyrene micro/nano particles impact the release of NOM during the aging of flocs formed by aluminum-based coagulants Al13 and AlCl3. The results elucidated that nano-particles with small particle sizes and agglomerative states are more likely to interact with coagulants. After 7 years of floc aging, the DOC content of the nano system decreased by more than 40%, while the micron system did not change significantly. During coagulation, the benzene rings in polystyrene particles form complexes with electrophilic aluminum ions through π-bonding, creating new Al-O bonds. NOM tends to adsorb at micro/nano plastic interfaces due to hydrophobic interactions and conformational entropy. In the aging process, the structure of PS-Al13 or PS-AlCl3 flocs and the functional groups on the surface of micro/nano plastics control the absorption and release of organic matter through hydrophobic, van der Waals forces, hydration, and polymer bridging. In the system with the addition of nano plastics, several DBPs such as TCAA, DCAA, TBM, DBCM and nitrosamines were reduced by more than 50%. The reaction order of different morphological structures and surface functional groups of microplastics to Al13 and AlCl3 systems is aromatic C-H > C-OH > C-O > NH2 > aromatic CC > aliphatic C-H and C-O>H-CO> NH2 >C-OH> aliphatic C-H. The results provided a new sight to explore the effect of micro/nano plastics on the release of NOM during flocs aging.

Post Natal Microbial and Metabolite Transmission: The Path from Mother to Infant

The entero-mammary pathway is a specialized route that selectively translocates bacteria to the newborn's gut, playing a crucial role in neonatal development. Previous studies report shared bacterial and archaeal taxa between human milk and neonatal intestine. However, the functional implications for neonatal development are not fully understood due to limited evidence. This study aimed to identify and characterize the microbiota and metabolome of human milk, mother, and infant stool samples using high-throughput DNA sequencing and FT-ICR MS methodology at delivery and 4 months post-partum. Twenty-one mothers and twenty-five infants were included in this study. Our results on bacterial composition suggest vertical transmission of bacteria through breastfeeding, with major changes occurring during the first 4 months of life. Metabolite chemical characterization sheds light on the growing complexity of the metabolites. Further data integration and network analysis disclosed the interactions between different bacteria and metabolites in the biological system as well as possible unknown pathways. Our findings suggest a shared bacteriome in breastfed mother-neonate pairs, influenced by maternal lifestyle and delivery conditions, serving as probiotic agents in infants for their healthy development. Also, the presence of food biomarkers in infants suggests their origin from breast milk, implying selective vertical transmission of these features.

Effect of Land Use Change on Molecular Composition and Concentration of Organic Matter in an Oxisol

Land use change from native vegetation to cropping can significantly affect the quantity and quality of soil organic matter (SOM). However, it remains unclear how the chemical composition of SOM is affected by such changes. This study employed a sequential chemical extraction to partition SOM from an Oxisol into several distinct fractions: water-soluble fractions (ultrapure water (W)), organometal complexes (sodium pyrophosphate (PP)), short-range ordered (SRO) oxides (hydroxylamine-HCl (HH)), and well-crystalline oxides (dithionite-HCl (DH)). Coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS), the impact of land use change on the molecular composition of different OM fractions was investigated. Greater amounts of OM were observed in the PP and HH fractions compared to other fractions, highlighting their importance in SOM stabilization. The composition of different OM fractions varied based on extracted phases, with lignin-like and tannin-like compounds being prevalent in the PP and HH fractions, while aliphatic-like compounds dominated in the DH fraction. Despite changes in the concentration of each OM fraction from native vegetation to cropping, there was little influence of land use change on the molecular composition of OM associated with different mineral phases. No significant selective loss or preservation of organic carbon compounds was observed, indicating the composition of SOM remained unchanged.

Structural characterization of the extracellular stalk material of the diatom Didymosphenia geminata

The study represents new bioanalytical characterization of mainly organic components of the poorly investigated extracellular polymeric substances (EPS) of the enigmatic diatom Didymosphenia geminata, an invasive, worldwide expanding species endangering diverse ecosystems. This microalga attaches its siliceous cells to rocky substrates using fibrous stalks, which are made of an EPS-based matrix stabilized by crystalline calcite. The EPS were analyzed using selected methods, including microscopic, spectroscopic, and spectrometric techniques. We identified diverse types of biomolecules. The presence of lipids, condensed aromatics, and heteroaromatic compounds in the EPS has been confirmed using high-resolution mass spectrometry (HR-MS). Additionally, both sulfur-containing functionalities and carboxylic acids were determined too using infrared (IR) spectroscopy and nuclear magnetic resonance (NMR) spectroscopy. For the first time, lignin compounds have been detected as one of the components of the EPS of the D. geminata diatom, using HR-MS and fluorescence microscopy (FM) in combination with specific staining techniques. By increasing the understanding of the chemistry and structural features of the stalks, we aim to develop potential applications and methods for removing these stalks from affected regions in the future, or, alternatively, to use them as a large-scale source of sustainable biocomposite material.

Impact of Saccharomyces cerevisiae yeast inoculation mode on wine composition

Inoculation modes are known to affect yeast behavior. Here, we characterized the impact of ADY and pre-culturing on the composition of the resulting wine, fermented by four commercial strains of Saccharomyces cerevisiae. Classical oenological parameters were not affected by the yeast inoculation mode. Using an untargeted metabolomic approach, a significant distinction in wine composition was noted regardless of the strain between the two inoculation modes, each associated with a specific metabolomic signature. 218 and 895 biomarkers were annotated, respectively, for ADYs associated with the preservation of wine polyphenols, and for pre-cultures related to the modulation of yeast nitrogen metabolism. Volatilome analysis revealed that the ester family was that most impacted by the inoculation mode whatever the strain. Ester production was enhanced in ADY condition. For the first time, the complete reprogramming of the yeast metabolism was revealed as a function of yeast preparation, which significantly impacts its volatilome and exometabolome.

Utilising Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to track the oxidation of lignin by an alkaliphilic laccase

Lignin is a complex heteroaromatic polymer which is one of the most abundant and diverse biopolymers on the planet. It comprises approximately one third of all woody plant matter, making it an attractive candidate as an alternative, renewable feedstock to petrochemicals to produce fine chemicals. However, the inherent complexity of lignin makes it difficult to analyse and characterise using common analytical techniques, proving a hindrance to the utilisation of lignin as a green chemical feedstock. Herein we outline the tracking of lignin degradation by an alkaliphilic laccase in a semi-quantitative manner using a combined chemical analysis approach using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to characterise shifts in chemical diversity and relative abundance of ions, and NMR to highlight changes in the structure of lignin. Specifically, an alkaliphilic laccase was used to degrade an industrially relevant lignin, with compounds such as syringaresinol being almost wholly removed (95%) after 24 hours of treatment. Structural analyses reinforced these findings, indicating a >50% loss of NMR signal relating to β-β linkages, of which syringaresinol is representative. Ultimately, this work underlines a combined analytical approach that can be used to gain a broader semi-quantitative understanding of the enzymatic activity of laccases within a complex, non-model mixture.

Estuarine hydrodynamic processes driving the molecular changes of terrestrial dissolved organic nitrogen: From mixing to biological modification

Estuaries receive substantial amounts of terrestrial dissolved organic nitrogen (tDON), which will be transported from the freshwater to the oceanic terminus through vigorous exchange processes. However, the intricate migration and transformation dynamics of tDON during this transportation, particularly at a molecular level, remain constrained. To address this knowledge gap, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was used for the analysis of DON molecular composition in the Pearl River Estuary (PRE), a river-dominated estuarine system influenced by intensified anthropogenic activities in southern China. The results showed a pronounced spatial-temporal variation in DON concentration in the study area. At the molecular level, tDON exhibited reduced unsaturation and aromaticity, coupled with an elevated abundance of DON compounds containing one‑nitrogen atom (1 N-DON, 53.17 %) and compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur (CHONS) (27.46 %). It was evident that lignin was depleted while more oxygenated tannin compounds were generated in the freshwater-seawater mixing zone. This transformation is attributed to heightened biological activities, likely influenced by the priming effect of terrestrial nutrient inputs. In summer, the prevailing plume combined with biological activities in the strong mixing area and outer estuary increased the abundance of 3 N-DON molecules and a concurrent rise in the abundance of DON compounds containing only carbon, hydrogen, oxygen, and nitrogen (CHON), DON compounds containing carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphorus (CHONSP), and CHONS. This trend also underscores the expanding role of marine plankton and microbes in the utilization of DON compounds containing carbon, hydrogen, oxygen, nitrogen, and phosphorus (CHONP). These findings provide details of tDON transformation processes at the molecular level in a river-dominated estuary and underline the estuarine hydrodynamics involved in transporting and altering DON within the estuary.

Inhibition of anaerobic digestion by various ammonia sources resulted in subtle differences in metabolite dynamics

The impact of ammonia on anaerobic digestion performance and microbial dynamics has been extensively studied, but the concurrent effect of anions brought by ammonium salt should not be neglected. This paper studied this effect using metabolomics and a time-course statistical framework. Metabolomics provides novel perspectives to study microbial processes and facilitates a more profound understanding at the metabolic level. The advanced statistical framework enables deciphering the complexity of large metabolomics data sets. More specifically, a series of lab-scale batch reactors were set up with different ammonia sources added. Samples of nine time points over the degradation were analyzed with liquid chromatography-mass spectrometry. A filtering procedure was applied to select the promising metabolomic peaks from 1262 peaks, followed by modeling their intensities across time. The metabolomic peaks with similar time profiles were clustered, evidencing the correlation of different biological processes. Differential analysis was performed to seek the differences in metabolite dynamics caused by different anions. Finally, tandem mass spectrometry and metabolite annotation provided further information on the molecular structure and possible metabolic pathways. For example, the consumption of 5-aminovaleric acid, a short-chain fatty acid obtained from l-lysine degradation, was slowed down by phosphates. Overall, by investigating the effect of anions on anaerobic digestion, our study demonstrated the effectiveness of metabolomics in providing detailed information in a set of samples from different experimental conditions. With the statistical framework, the approach enables capturing subtle differences in metabolite dynamics between samples while accounting for the differences caused by time variations.

Competition for Nitrogen Resources: An Explanation of the Effects of a Bioprotective Strain Metschnikowia pulcherrima on the Growth of Hanseniaspora Genus in Oenology

As a biological alternative to the antimicrobial action of SO2, bioprotection has been proposed to winemakers as a means to limit or prevent grape musts microbial alteration. Competition for nitrogenous nutrients and for oxygen are often cited as potential explanations for the effectiveness of bioprotection. This study analyses the effect of a bioprotective M. pulcherrima strain on the growth of one H. valbyensis strain and one H. uvarum strain. Bioprotection efficiency was observed only against H. valbyensis inoculated at the two lowest concentrations. These results indicate a potential species-dependent efficiency of the bioprotective strain and a strong impact of the initial ratio between bioprotective and apiculate yeasts. The analysis of the consumption of nitrogen compounds revealed that leucine, isoleucine, lysine and tryptophan were consumed preferentially by all three strains. The weaker assimilation percentages of these amino acids observed in H. valbyensis at 24 h growth suggest competition with M. pulcherrima that could negatively affects the growth of the apiculate yeast in co-cultures. The slowest rate of O2 consumption of H. valbyensis strain, in comparison with M. pulcherrima, was probably not involved in the bioprotective effect. Non-targeted metabolomic analyses of M. pulcherrima and H. valbyensis co-culture indicate that the interaction between both strains particularly impact lysin and tryptophan metabolisms.

LC-HRMS-Driven Computational Toolbox to Assess Extraction Protocols Dedicated to Untargeted Analysis: How to Ease Analyzing Pesticide-Contaminated Soils?

Metabolomics is a powerful approach that allows for high throughput analysis and the acquisition of large biochemical data. Nonetheless, it still faces several challenging requirements, such as the development of optimal extraction and analytical methods able to respond to its high qualitative and quantitative requisites. Hence, the objective of the present article is to suggest a LC-HRMS-based untargeted profiling approach aiming to provide performant tools that help assess the performance and the quality of extraction methods. It is applied in a herbicide-contaminated soil metabolomics context. The trifactorial experimental design consists of 150 samples issued from five different extraction protocols, two types of soils, and three contamination conditions (contaminated soils with two different formulated herbicides against uncontaminated soils). Four performance and quality criteria are investigated using adapted LC-HRMS-driven computational tools. First, 861 metabolic features are annotated, and then the width of metabolome coverage and quantitative performance of the five different extraction protocols are assessed in all samples using various optimized configurations of heatmaps as well as van Krevelen diagrams. Then, the reproducibility of LC-HRMS profiles issued from the five extractions is studied by two different approaches: Euclidean distances and relative standard deviations. The two methods are examined and compared. Their advantages and limitations are thus discussed. After, the capacity of the different extractions to discriminate between contaminated and uncontaminated soils will be evaluated using orthogonal projections to latent structures-discriminant analysis. Different data scaling parameters are tested, and the results are explored and discussed. All of the suggested computational and visualization tools are performed using public-access platforms or open-source software. They can be readapted by metabolomics developers and users according to their study contexts and fields of application.

Using landfill leachate to indicate the chemical and biochemical activities in elevated temperature landfills

Landfill leachate properties contain important information and can be a unique indicator for the chemical and biochemical activities in landfills. In the recent decade, more landfills are experiencing elevated temperature, causing an imbalance in the decomposition of solid waste and affecting the properties of the landfill leachate. This study analyzes the properties of leachate from two landfills that were experiencing elevated temperature (ETLFs), samples were collected from both elevated temperature impacted and non-impacted areas in each landfill. The accumulation of volatile fatty acids (VFA) in leachates from elevated temperature impacted areas of both landfill sites revealed that methanogenesis was inhibited by the elevated temperature, which was further confirmed by the more acidic pH, higher H/C elemental ratio, and lower degree of aromaticity of the elevated temperature impacted leachates. Also, carbohydrates depletion indicated possible enhancement of hydrolysis and acidogenesis by elevated temperature, which was supported by compositional comparison of isolated acidic species by negative-ion electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICRMS) at 21 T derived from both elevated temperature impacted and non-impacted areas in the same landfill site. Furthermore, leachate organics fractionation showed that leachates not impacted by elevated temperature contain less hydrophilic fraction and more humic fraction than elevated temperature-impacted leachates for both ETLFs.

Internal exposure potential of water-soluble organic molecules in urban PM2.5 evaluated by non-covalent adductome of human serum albumin

Water-soluble organic molecules (WSOMs) in inhaled PM2.5 can readily translocate from the lungs into the blood circulation, facilitating their distribution to and health effects on distant organs and tissues in the human body. Human serum albumin (HSA), the most abundant protein carrier in the blood, readily binds exogenous substances to form non-covalent adducts and subsequently transports them throughout the circulatory system, thereby indicating their internal exposure. The direct internal exposure of WSOMs in PM2.5 needs to be understood. In this study, the non-covalent HSA-WSOM adductome was developed as a dosimeter to evaluate the internal exposure potential of WSOMs in urban PM2.5. The WSOM composition was acquired from non-target high-resolution mass spectrometry analysis coupled with multiple ionizations. The binding level of HSA-WSOM non-covalent adducts was obtained from surface plasma resonance. Machine learning combined WSOM composition and the binding level of HSA-WSOM non-covalent adducts to screen bindable (also internalizable) WSOMs. The concentration of WSOM ranged from 4 to 13 μg/m3 during our observation period. Of the 17,513 mass spectral features detected, 9,484 contributed to the non-covalent adductome and possessed the internal exposure potential. 102 major contributors accounted for 90.6 % of the HSA-WSOM binding level. The fraction of internalizable WSOMs in PM2.5 varied from 11.9 % to 61.3 %, averaging 26.2 %. WSOMs that have internal exposure potential were primarily lignin-like and lipid-like substances. The HSA-WSOMs non-covalent adductome represents direct internal exposure potential, which can provide crucial insights into the molecular diagnosis of PM2.5 exposure and precise assessments of PM2.5 health effects.

Comprehending the practical implementation of permanganate and ferrate for water remediation in complex water matrices

Most previous studies examined permanganate or ferrate oxidation using various emerging pollutants (EPs) spiked in ultrapure water with concentrations of orders-of-magnitude higher than those in natural waters. In present study, we assessed the efficiency of permanganate and ferrate (with ozone as a comparison) at mg L-1 level to remove selected EPs at μg L-1 level in complex water matrices. The efficiency of permanganate and ferrate is more easily affected by the humic acid in synthetic water or dissolved organic matter (DOM) in natural river water compared to ozone. Experiment results revealed that humic acid or DOM were not mineralized by oxidants, but changed in compositional nature, including decreases in the aromaticity, electron-donating capacity, and average molecular weight. At molecular level, condensed aromatic, lignin-like, and tannin-like components in humic acid and DOM are the critical sites being attacked by permanganate or ferrate, the alkene groups and aromatic structures were oxidized predominantly to carboxylic acids. Overall, the present study provided insights into the performance of permanganate and ferrate used for EPs treatment under realistic conditions, as well as alternations of DOM that can be expected following exposure to these oxidants.

Solid-Phase Extraction at High pH as a Promising Tool for Targeted Isolation of Biologically Active Fractions of Humic Acids

A search for novel sources of biologically active compounds is at the top of the agenda for biomedical technologies. Natural humic substances (HSs) contain a large variety of different chemotypes, such as condensed tannins, hydrolyzable tannins, terpenoids, lignins, etc. The goal of this work was to develop an efficient separation technique based on solid-phase extraction (SPE) for the isolation of narrow fractions of HS with higher biological activity compared to the initial material. We used lignite humic acid as the parent humic material, which showed moderate inhibition activity toward beta-lactamase TEM 1 and antioxidant activity. We applied two different SPE techniques: the first one was based on a gradient elution with water/methanol mixtures of the humic material sorbed at pH 2, and the second one implied separation by a difference in the pKa value by the use of sequential sorption of HS at pH from 8 to 3. SPE cartridges Bond Elute PPL (Agilent) were used in the fractionation experiments. The first and second techniques yielded 9 and 7 fractions, respectively. All fractions were characterized using high-resolution mass spectrometry and biological assays, including the determination of beta-lactamase (TEM 1) inhibition activity and antioxidant activity. The acidity-based separation technique demonstrated substantial advantages: it enabled the isolation of components, outcompeting the initial material at the first step of separation (sorption at pH 8). It showed moderate orthogonality in separation with regard to the polarity-based technique. Good perspectives are shown for developing a 2D separation scheme using a combination of polarity and acidity-based approaches to reduce structural heterogeneity of the narrow fractions of HS.

Chemometric Combination of Ultrahigh Resolving Mass Spectrometry and Nuclear Magnetic Resonance Spectroscopy for a Structural Characterization of Lignin Compounds

In recent years, the potential of lignins as a resource for material-based applications has been highlighted in many scientific and nonscientific publications. But still, to date, a lack of detailed structural knowledge about this ultracomplex biopolymer undermines its great potential. The chemical complexity of lignin demands a combination of different, powerful analytical methods, in order to obtain these necessary information. In this paper, we demonstrate a multispectroscopic approach using liquid-state and solid-state Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and nuclear magnetic resonance (NMR) spectroscopy to characterize a fractionated LignoBoost lignin. Individual FT-ICR-MS, tandem MS, and NMR results helped to determine relevant information about the different lignin fractions, such as molecular weight distributions, oligomer sizes, linkage types, and presence of specific functional groups. In addition, a hetero spectroscopic correlation approach was applied to chemometrically combine MS, MS/MS, and NMR data sets. From these correlation analyses, it became obvious that a combination of tandem MS and NMR data sets gives the opportunity to comprehensively study and describe the general structure of complex biopolymer samples. Compound-specific structural information are obtainable, if this correlation approach is extended to 1D-MS and NMR data, as specific functional groups or linkages are verifiable for a defined molecular formula. This enables structural characterization of individual lignin compounds without the necessity for tandem MS experiments. Hence, these correlation results significantly improve the depth of information of each individual analysis and will hopefully help to structurally elucidate entire lignin structures in the near future.

Effects of reservoir construction on optical and molecular characteristics of dissolved organic matter in a typical P-contaminated river

The source and composition characteristics of dissolved organic matter (DOM) are crucial to identify and evaluate the sources of pollution in the watershed. The construction of reservoirs changes the hydrological condition and pollutant fate of the river. However, the effects of reservoirs' construction on DOM in the watershed and the underlying mechanisms are still unclear. This study aims to examine and compare the characteristics of DOM in reservoirs and streams in the Huangbai River, a typical reservoir-affected and P-contaminated river within the Yangtze River catchment. The results showed that DOM in reservoirs was characterized by more contribution from autochthonous source, under the influence of reservoirs' construction; while, DOM in rivers was mainly originated from terrestrial input. Reservoirs had more lipid-like and protein-like compounds, while rivers contained more oxy-aromatic-like compounds. The percentage of CHOP molecules in reservoirs was significantly higher than that in rivers. The underlying mechanism is that more suitable conditions were created for plankton to grow after constructing reservoirs, which converted inorganic orthophosphate into organic phosphorus, and over time, organic phosphorus was gradually enriched in reservoirs, which exacerbated the risk of eutrophication in the reservoir water body. This study can provide theoretical support for monitoring and evaluation of water quality in reservoir-affected rivers.

Must protection, sulfites versus bioprotection: A metabolomic study

The reduction of chemical inputs in wine has become one of the main challenges of the wine industry. One of the alternatives to sulfites developed is bioprotection, which consists in using non-Saccharomyces strains to prevent microbial deviation. However, the impact of substituting sulfites by bioprotection on the final wine remains poorly studied. For the first time, we characterized this impact on Chardonnay wine through an integrative approach. Interestingly, physico-chemical analysis did not reveal any difference between both treatments regarding classical oenological parameters. Nevertheless, bioprotection did not seem to provide as much protection against oxidation as sulfites, as observed through phenolic compound analysis. At a deeper level, untargeted metabolomic analyses revealed substantial changes in wine composition according to must treatment. In particular, the specific footprint of each treatment revealed an impact on nitrogen-containing compounds. This observation could be related to modifications in S. cerevisiae metabolism, in particular amino acid biosynthesis and tryptophan metabolism pathways. Thus, the type of must treatment seemed to impact metabolic fluxes of yeast differently, leading to the production of different compounds. For example, we observed glutathione and melatonin, compounds with antioxidant properties, which were enhanced with sulfites, but not with bioprotection. However, despite substantial modifications in wines regarding their chemical composition, the change in must treatment did not seem to impact the sensory profile of wine. This integrative approach has provided relevant new insights on the impact of sulfite substitution by bioprotection on Chardonnay wines.

Bioprotection Efficiency of Metschnikowia Strains in Synthetic Must: Comparative Study and Metabolomic Investigation of the Mechanisms Involved

Three Metschnikowia strains marketed as bioprotection yeasts were studied to compare their antimicrobial effect on a mixture of two Hanseniaspora yeast strains in synthetic must at 12 °C, mimicking pre-fermentative maceration by combining different approaches. The growth of the different strains was monitored, their nitrogen and oxygen requirements were characterised, and their metabolomic footprint in single and co-cultures studied. Only the M. fructicola strain and one M. pulcherrima strains colonised the must and induced the rapid decline of Hanseniaspora. The efficiency of these two strains followed different inhibition kinetics. Furthermore, the initial ratio between Metschnikowia and Hanseniaspora was an important factor to ensure optimal bioprotection. Nutrient consumption kinetics showed that apiculate yeasts competed with Metschnikowia strains for nutrient accessibility. However, this competition did not explain the observed bioprotective effect, because of the considerable nitrogen content remaining on the single and co-cultures. The antagonistic effect of Metschnikowia on Hanseniaspora probably implied another form of amensalism. For the first time, metabolomic analyses of the interaction in a bioprotection context were performed after the pre-fermentative maceration step. A specific footprint of the interaction was observed, showing the strong impact of the interaction on the metabolic modulation of the yeasts, especially on the nitrogen and vitamin pathways.

Automatization of metabolite extraction for high-throughput metabolomics: case study on transgenic isoprene-emitting birch

Metabolomics studies are becoming increasingly common for understanding how plant metabolism responds to changes in environmental conditions, genetic manipulations and treatments. Despite the recent advances in metabolomics workflow, the sample preparation process still limits the high-throughput analysis in large-scale studies. Here, we present a highly flexible robotic system that integrates liquid handling, sonication, centrifugation, solvent evaporation and sample transfer processed in 96-well plates to automatize the metabolite extraction from leaf samples. We transferred an established manual extraction protocol performed to a robotic system, and with this, we show the optimization steps required to improve reproducibility and obtain comparable results in terms of extraction efficiency and accuracy. We then tested the robotic system to analyze the metabolomes of wild-type and four transgenic silver birch (Betula pendula Roth) lines under unstressed conditions. Birch trees were engineered to overexpress the poplar (Populus × canescens) isoprene synthase and to emit various amounts of isoprene. By fitting the different isoprene emission capacities of the transgenic trees with their leaf metabolomes, we observed an isoprene-dependent upregulation of some flavonoids and other secondary metabolites as well as carbohydrates, amino acid and lipid metabolites. By contrast, the disaccharide sucrose was found to be strongly negatively correlated to isoprene emission. The presented study illustrates the power of integrating robotics to increase the sample throughput, reduce human errors and labor time, and to ensure a fully controlled, monitored and standardized sample preparation procedure. Due to its modular and flexible structure, the robotic system can be easily adapted to other extraction protocols for the analysis of various tissues or plant species to achieve high-throughput metabolomics in plant research.

Ultrahigh performance LC/FT-MS non-targeted screening for biomass burning organic aerosol with MZmine2 and MFAssignR

In recent years, ultrahigh performance liquid chromatography Fourier transform mass spectrometry (LC/FT-MS) based non-targeted screening (NTS) methods have become increasingly popular for comprehensive analysis of complex organic mixtures. However, applying these methods for environmental complex mixture analysis is challenging due to the extreme complexity of natural samples and a lack of standard samples or surrogates for environmental complex mixtures. Furthermore, limited molecular markers in the databases and insufficient data processing software workflows make the application of these methods more challenging for environmental complex mixtures. In this work, we implement a new NTS data processing workflow to process data collected from ultrahigh performance liquid chromatography and Fourier transform Orbitrap Elite Mass Spectrometry (LC/FT-MS) by combining MZmine2 and MFAssignR, two opensource data processing tools and commercial Mesquite liquid smoke as a surrogate for biomass burning organic aerosol. MZmine2.53 data extraction followed MFAssignR molecular formula assignment offered noise free and highly accurate 1733 individual molecular formulas presented in liquid smoke with 4906 molecular species, including isomers. The results of this new approach were consistent with the results of direct infusion FT-MS analysis confirming its reliability. Over 90% of the molecular formulas presented in mesquite liquid smoke were matched with the molecular formulas of ambient biomass burning organic aerosol. This suggests the potential use of commercial liquid smoke is an acceptable surrogate for biomass burning organic aerosol research. The presented method significantly improves the identification of the molecular composition of biomass burning organic aerosol by successfully addressing some of the limitations related to the data analysis and giving a semi quantitative insight into the analysis.

Influence of Air Mass Source Regions on Signatures of Surface-Active Organic Molecules in Size Resolved Atmospheric Aerosol Particles

The physical and chemical properties of atmospheric aerosol particles depend on their sources and lifetime in the atmosphere. In coastal regions, sources may include influences from marine, continental, anthropogenic, and natural emissions. In this study, particles in ten diameter-size ranges were collected, and particle number size distributions were measured, at Skidaway Island, GA in May and June 2018. Based on air mass back trajectories and concentrations of major ions in the particles, the air mass source regions were identified as Marine Influenced, Mixed, and Continental Influenced. Organic molecules were extracted from the particles using solid-phase extraction and characterized using tensiometry and high-resolution mass spectrometry. The presence of surfactants was confirmed in the extracts through the observation of significant surface tension depressions. The organic formulas contained high hydrogen-to-carbon (H/C) and low oxygen-to-carbon (O/C) ratios, similar to surfactants and lipid-like molecules. In the Marine Influenced particles, the fraction of formulas identified as surfactant-like was negatively correlated with minimum surface tensions; as the surfactant fraction increased, the surface tension decreased. Analyses of fatty acid compounds demonstrated that organic compounds extracted from the Marine Influenced particles had the highest carbon numbers (18), compared to those of the Mixed (15) and Continental Influenced (9) particles. This suggests that the fatty acids in the Continental Influenced particles may have been more aged in the atmosphere and undergone fragmentation. This is one of the first studies to measure the chemical and physical properties of surfactants in size-resolved particles from different air mass source regions.

Exposomic Biomonitoring of Polyphenols by Non-Targeted Analysis and Suspect Screening

Polyphenols, prevalent in plants and fungi, are investigated intensively in nutritional and clinical settings because of their beneficial bioactive properties. Due to their complexity, analysis with untargeted approaches is favorable, which typically use high-resolution mass spectrometry (HRMS) rather than low-resolution mass spectrometry (LRMS). Here, the advantages of HRMS were evaluated by thoroughly testing untargeted techniques and available online resources. By applying data-dependent acquisition on real-life urine samples, 27 features were annotated with spectral libraries, 88 with in silico fragmentation, and 113 by MS1 matching with PhytoHub, an online database containing >2000 polyphenols. Moreover, other exogenous and endogenous molecules were screened to measure chemical exposure and potential metabolic effects using the Exposome-Explorer database, further annotating 144 features. Additional polyphenol-related features were explored using various non-targeted analysis techniques including MassQL for glucuronide and sulfate neutral losses, and MetaboAnalyst for statistical analysis. As HRMS typically suffers a sensitivity loss compared to state-of-the-art LRMS used in targeted workflows, the gap between the two instrumental approaches was quantified in three spiked human matrices (urine, serum, plasma) as well as real-life urine samples. Both instruments showed feasible sensitivity, with median limits of detection in the spiked samples being 10-18 ng/mL for HRMS and 4.8-5.8 ng/mL for LRMS. The results demonstrate that, despite its intrinsic limitations, HRMS can readily be used for comprehensively investigating human polyphenol exposure. In the future, this work is expected to allow for linking human health effects with exposure patterns and toxicological mixture effects with other xenobiotics.

Sugars and Organic Acids in 25 Strawberry Cultivars: Qualitative and Quantitative Evaluation

(1) The nutritional quality of strawberry (Fragaria × ananassa Duch) fruits, among others, is largely maintained by the presence of soluble sugars and organic acids. As the primary products of photosynthesis, they are energy depots in plants, necessary for the construction of cell constituents, but also serve as precursors of aromatic compounds and signaling molecules. (2) In this study, fruits of 25 strawberry cultivars were qualitatively and quantitatively characterized concerning individual sugars and organic acids by HPLC, FT-ICR-MS, and MS imaging analysis. In addition, the total quality index (TQI), as a novel mathematical model, was used to compare all individual parameters evaluated to obtain a quantitative single score, as an indicator of overall fruit quality. (3) Regardless of a large number of cultivars and monitored parameters that were studded, several cultivars stood out in terms of selected primary metabolites, such as 'Rumba', 'Jeny', and 'Sandra', while the latter had the best TQI score. (4) Intercultivar variations in sugars and organic acids profiles, along with other bioactive compounds, should be considered for selection of promising cultivars with improved naturally occurring nutraceutical traits. Besides the search for a pleasant taste, increased awareness of healthy nutrition resulted in heightening consumer demand for high-quality fruit.

Humid Evolution of Haze in the Atmosphere of Super-Earths in the Habitable Zone

Abstract Photochemical hazes are expected to form and significantly contribute to the chemical and radiative balance of exoplanets with relatively moderate temperatures, possibly in the habitable zone of their host star. In the presence of humidity, haze particles might thus serve as cloud condensation nuclei and trigger the formation of water droplets. In the present work, we are interested in the chemical impact of such a close interaction between photochemical hazes and humidity on the organic content composing the hazes and on the capacity to generate organic molecules with high prebiotic potential. For this purpose, we explore experimentally the sweet spot by combining N-dominated super-Earth exoplanets in agreement with Titan's rich organic photochemistry and humid conditions expected for exoplanets in habitable zones. A logarithmic increase with time is observed for the relative abundance of oxygenated species, with O-containing molecules dominating after 1 month only. The rapidity of the process suggests that the humid evolution of N-rich organic haze provides an efficient source of molecules with high prebiotic potential.

Molecular signatures of soil-derived dissolved organic matter constrained by mineral weathering

Dissolved organic matter (DOM) in soils drives biogeochemical cycling and soil functions in different directions depending on its molecular signature. Notably, there is a distinct paucity of information concerning how the molecular signatures of soil DOM vary with different degrees of weathering across wide geographic scales. Herein, we resolved the DOM molecular signatures from 22 diverse Chinese reference soils and linked them with soil organic matter and weathering-related mineralogical properties. The mixed-effects models revealed that the yields of DOM were determined by soil organic carbon content, whereas the molecular signature of DOM was primarily constrained by the weathering-related dimension. The soil weathering index showed a positive effect on the lability and a negative effect on the aromaticity of DOM. Specifically, DOM in highly weathered acidic soils featured more amino sugars, carbohydrates, and aliphatics, as well as less O-rich polyphenols and condensed aromatics, thereby conferring a higher DOM biolability and lower DOM aromaticity. This study highlights the dominance of the weathering-related dimension in constraining the molecular signatures and potential functions of DOM in soils across a wide geographic scale.

Molecular behavior and interactions with microbes during anaerobic degradation of bio-derived DOM in waste leachate

It is the key to control bio-derived dissolved organic matters (DOM) in order to reduce the effluent concentration of wastewater treatment, especially for waste leachate with high organic contaminants. In the present study, the anaerobic degradation of aerobically stabilized DOM was investigated with DOM substrate isolated through electrodialysis. The degradation of bio-derived DOM was confirmed by reduction of 15% of total organic carbon in 100 days. We characterized the molecular behavior of bio-derived DOM by coupling molecular and biological information analysis. Venn based Sankey diagram of mass features showed the transformation of bio-derived DOM mass features. Occurrence frequency analysis divided mass features into six categories so as to distinguish the fates of intermediate metabolites and persistent compounds. Reactivity continuum model and machine learning technologies realized the semi-quantitative determination on the kinetics of DOM mass features in the form of pseudo-first order, and confirmed the reduction of inert mass features. Furthermore, network analysis statistically establish relationship between DOM mass features and microbes to identify the active microbes that are able to utilize bio-derived DOM. This work confirmed the biological technology is still effective in controlling recalcitrant bio-derived DOM during wastewater treatment.

Enrichment and analysis methods for trace dissolved organic carbon in reverse osmosis effluent: A review

Reverse osmosis (RO) is an essential unit for producing high-quality ultrapure water. The increasingly severe water shortage and water quality deterioration result in reclaimed water as an alternative source for ultrapure water production. However, when using reclaimed water as water sources, the dissolved organic carbon (DOC) in RO permeate exhibits higher concentration and more sophisticated components than when using clean water sources, thus affecting the effluent quality of ultrapure water and the effectiveness of subsequent treatment processes. To optimize the treatment processes, it is crucial to analyze the components of DOC. This review summarizes the enrichment and analysis methods of trace organic matter, and provides recommendations for the analysis and characterization of DOC in RO permeate. The study summarizes the operating conditions and enrichment properties of different enrichment methods, including solid-phase extraction, liquid-liquid extraction, purge-and-trap, lyophilization and rotary evaporation for low-concentration organic compounds, compares the applicability and limitations of different enrichment methods, and proposes the principles for the selection of enrichment methods. In this review, we discuss the application of mass spectrometry (including Fourier transform ion cyclotron resonance mass spectrometry) in the analysis of DOC components, and focus on data processing as the key procedure in analysis of DOC in RO permeate. Despite the advantages of mass spectrometry, an applicable workflow and open-source database are required to improve the reliability of the analysis. The treatability properties of DOC are suggested to be determined by analyzing the component characteristics or in combination with common removal techniques. This study provides theoretical support for a comprehensive analysis of DOC in RO permeates to improve the removal effect.

Thiamine and Biotin: Relevance in the Production of Volatile and Non-Volatile Compounds during Saccharomyces cerevisiae Alcoholic Fermentation in Synthetic Grape Must

Vitamins are major cofactors to numerous key metabolic pathways in enological yeasts, and both thiamine and biotin, notably, are believed to be essential to yeast fermentation and growth, respectively. In order to further assess and clarify their role in winemaking, and in the resulting wine, alcoholic fermentations of a commercial Saccharomyces cerevisiae active dried yeast were conducted in synthetic media containing various concentrations of both vitamins. Growth and fermentation kinetics were monitored and proved the essential character of biotin in yeast growth, and of thiamine in fermentation. The synthetic wine volatile compounds were quantified, and notable influences of both vitamins appeared, through a striking positive effect of thiamine on the production of higher alcohols, and of biotin on fatty acids. Beyond the evidence of this influence on fermentations and on the production of volatiles, this work proves, for the first time, the impact held by vitamins on wine yeasts' exometabolome, investigated through an untargeted metabolomic analysis. This highlighted chemical differences in the composition of synthetic wines through a notably marked influence of thiamine on 46 named S. cerevisiae metabolic pathways, and especially in amino acid-associated metabolic pathways. This provides, overall, the first evidence of the impact held by both vitamins on the wine.

Characterization of Corn Silk Extract Using HPLC/HRMS/MS Analyses and Bioinformatic Data Processing

In addition to having different biological activities of interest, corn silks play a role in the defense of plants. While benzoxamines and flavonoids have already been identified as molecules of plant defense and growth mechanisms, knowledge on the phytochemical composition of corn silk is lacking. Such knowledge would make it possible to better select the most effective varieties to improve resistance or bioactive properties. In this article, an approach was implemented to map a corn silk extract in two complementary ways. The first one involved working with UHPLC/HRMS data and Kendrick and van Krevelen plots to highlight a homologous series of compounds, such as lipids from 17 to 23 carbons, monoglycosylated flavonoids from 21 to 24 carbons, diglycosylated flavonoids of 26 to 28 carbons and organic acids of 14 to 19 carbons. The second way was to analyze the sample in UHPLC/HRMS² and to plot mass spectral similarity networks with the GNPS platform and Cytoscape software to refine identification. By combining the information obtained, we were able to propose an identification for 104 detected molecules, including 7 nitrogenous, 28 lipidic and 67 phenolic compounds, leading to the first detailed phytochemical analysis of corn silk extract.

Sodium arsenite-induced changes in the wood of esca-diseased grapevine at cytological and metabolomic levels

In the past, most grapevine trunk diseases (GTDs) have been controlled by treatments with sodium arsenite. For obvious reasons, sodium arsenite was banned in vineyards, and consequently, the management of GTDs is difficult due to the lack of methods with similar effectiveness. Sodium arsenite is known to have a fungicide effect and to affect the leaf physiology, but its effect on the woody tissues where the GTD pathogens are present is still poorly understood. This study thus focuses on the effect of sodium arsenite in woody tissues, particularly in the interaction area between asymptomatic wood and necrotic wood resulting from the GTD pathogens' activities. Metabolomics was used to obtain a metabolite fingerprint of sodium arsenite treatment and microscopy to visualize its effects at the histo-cytological level. The main results are that sodium arsenite impacts both metabolome and structural barriers in plant wood. We reported a stimulator effect on plant secondary metabolites in the wood, which add to its fungicide effect. Moreover, the pattern of some phytotoxins is affected, suggesting the possible effect of sodium arsenite in the pathogen metabolism and/or plant detoxification process. This study brings new elements to understanding the mode of action of sodium arsenite, which is useful in developing sustainable and eco-friendly strategies to better manage GTDs.

Impact of beaver ponds on biogeochemistry of organic carbon and nitrogen along a fire-impacted stream

Wildfires, which are increasing in frequency and severity in the western U.S., impact water quality through increases in erosion, and transport of nutrients and metals. Meanwhile, beaver populations have been increasing since the early 1900s, and the ponds they create slow or impound hydrologic and elemental fluxes, increase soil saturation, and have a high potential to transform redox active elements (e.g., oxygen, nitrogen, sulfur, and metals). However, it remains unknown how the presence of beaver ponds in burned watersheds may impact retention and transformation of chemical constituents originating in burned uplands (e.g., pyrogenic dissolved organic matter; pyDOM) and the consequences for downstream water quality. Here, we investigate the impact of beaver ponds on the chemical properties and molecular composition of dissolved forms of C and N, and the microbial functional potential encoded within these environments. The chemistry and microbiology of surface water and sediment changed along a stream sequence starting upstream of fire and flowing through multiple beaver ponds and interconnecting stream reaches within a burned high-elevation forest watershed. The relative abundance of N-containing compounds increased in surface water of the burned beaver ponds, which corresponded to lower C/N and O/C, and higher aromaticity as characterized by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The resident microbial communities lack the capacity to process such aromatic pyDOM, though genomic analyses demonstrate their potential to metabolize various compounds in the anaerobic sediments of the beaver ponds. Collectively, this work highlights the role of beaver ponds as biological "hotspots" with unique biogeochemistry in fire-impacted systems.

Microbe Regulates the Mineral Photochemical Activity and Organic Matter Compositions in Water

Photochemical reactions that widely occur in aquatic environments play important roles in carbon fate (e.g., carbon conversion and storage from organic matter) in ecosystems. Aquatic microbes and natural minerals further regulate carbon fate, but the processes and mechanisms remain largely unknown. Herein, the interaction between Escherichia coli and pyrite and its influence on the fate of carbon in water were investigated at the microscopic scale and molecular level. The results showed that saccharides and phenolic compounds in microbial extracellular polymeric substances helped remove pyrite surface oxides via electron transfer. After the removal of surface oxides on pyrite, the photochemical properties under visible-light irradiation were significantly decreased, such as reactive oxygen species and electron transfer capacity. Unlike the well-accepted theory of minerals protecting organic matter in the soil, the organic matter adsorbed on minerals preferred degradation due to the enhanced photochemical reactions in water. In contrast, the minerals transformed by microbes suppressed the decomposition of organic matter due to the passivation of the chemical structure and activity. These results highlight the significance of mineral chemical activity on organic matter regulated by microbes and provide insights into organic matter conversion in water.

New insights into the Van Krevelen diagram: Automated molecular formula determination from HRMS for a large chemical profiling of lichen extracts

INTRODUCTION

In recent years, LC-MS has become the golden standard for metabolomic studies. Indeed, LC is relatively easy to couple with the soft electrospray ionization. As a consequence, many tools have been developed for the structural annotation of tandem mass spectra. However, it is sometimes difficult to do data-dependent acquisition (DDA), especially when developing new methods that stray from the classical LC-MS workflow.

OBJECTIVE

An old tool from petroleomics that has recently gained popularity in metabolomics, the Van Krevelen diagram, is adapted for an overview of the molecular diversity profile in lichens through high-resolution mass spectrometry (HRMS).

METHODS

A new method is benchmarked against the state-of-the-art classification tool ClassyFire using a database containing most known lichen metabolites (n ≈ 2,000). Four lichens known for their contrasted chemical composition were selected, and extractions with apolar, aprotic polar, and protic polar solvents were performed to cover a wide range of polarities. Extracts were analyzed with direct infusion electrospray ionization mass spectrometry (DI-ESI-MS) and atmospheric solids analysis probe mass spectrometry (ASAP-MS) techniques to be compared with the chemical composition described in the literature.

RESULTS

The most common lichen metabolites were efficiently classified, with more than 90% of the molecules in some classes being matched with ClassyFire. Results from this method are consistent with the various extraction protocols in the present case study.

CONCLUSION

This approach is a rapid and efficient tool to gain structural insight regarding lichen metabolites analyzed by HRMS without relying on DDA by LC-MS/MS analysis. It may notably be of use during the development phase of novel MS-based metabolomic approaches.

Polymeric Compounds of Lingonberry Waste: Characterization of Antioxidant and Hypolipidemic Polysaccharides and Polyphenol-Polysaccharide Conjugates from Vaccinium vitis-idaea Press Cake

Lingonberry (Vaccinium vitis-idaea L.) fruits are important Ericaceous berries to include in a healthy diet of the Northern Hemisphere as a source of bioactive phenolics. The waste generated by the V. vitis-idaea processing industry is hard-skinned press cake that can be a potential source of dietary fiber and has not been studied thus far. In this study, water-soluble polysaccharides of V. vitis-idaea press cake were isolated, separated, and purified by ion-exchange and size-exclusion chromatography. The results of elemental composition, monosaccharide analysis, ultraviolet–visible and Fourier-transform infrared spectroscopy, molecular weight determination, linkage analysis, and alkaline destruction allowed us to characterize two polyphenol–polysaccharide conjugates (PPC) as neutral arabinogalactans cross-linked with monomeric and dimeric hydroxycinnamate residues with molecular weights of 108 and 157 kDa and two non-esterified galacturonans with molecular weights of 258 and 318 kDa. A combination of in vitro and in vivo assays confirmed that expressed antioxidant activity of PPC was due to phenolic-scavenged free radicals, nitrogen oxide, hydrogen peroxide, and chelate ferrous ions. Additionally, marked hypolipidemic potential of both PPC and acidic polymers bind bile acids, cholesterol, and fat, inhibit pancreatic lipase in the in vitro study, reduce body weight, serum level of cholesterol, triglycerides, low/high-density lipoprotein–cholesterol, and malondialdehyde, and increase the enzymatic activity of superoxide dismutase, glutathione peroxidase, and catalase in the livers of hamsters with a 1% cholesterol diet. Polysaccharides and PPC of V. vitis-idaea fruit press cake can be regarded as new antioxidants and hypolipidemic agents that can be potentially used to cure hyperlipidemic metabolic disorders.

Metabolomics analysis of unresolved molecular variability in stoichiometry dynamics of a stream dissolved organic matter

Broad molecular classification based on stoichiometric ratio relationships has been used extensively to characterize the chemical diversity of aquatic dissolved organic matter (DOM). However, variability in the molecular composition within this classification has remained elusive, thus limiting the interpretation of DOM dynamics, especially with respect to transport versus transformation patterns in response to hydrologic or landscape changes. Here, leveraging high-frequency spatiotemporal sampling during rainfall events at a Critical Zone Observatory project site in Clear Creek, Iowa, we apply a metabolomics-based analysis validated with fragmentation using tandem mass spectrometry to uncover patterns in the molecular features of the DOM composition that were not resolved by classification based on stoichiometric ratios in the chemical formulae. From upstream to downstream sites, beyond the increased aromaticity implied by changes in the stoichiometric ratios, we identified an increased abundance of flavonoids and other phenylpropanoids, two important subgroups of aromatic compounds. The stoichiometric analysis also proposed a localized decline in the abundance of lipid-like compounds, which we attributed specifically to medium-chain and short-chain fatty acids; other lipids such as long-chain fatty acids and sterol lipids remained unchanged. We further determined in-stream molecular transitions and specific compound degradation by capturing changes in the molecular masses of terpenoids, phenylpropanoids, fatty acids, and amino acids. In sum, the metabolomics analysis of the chemical formulae resolved molecular variability imprinted on the stoichiometric DOM composition to implicate key molecular subgroups underlying carbon transport and cycling dynamics in the stream.

Non-targeted screening of volatile organic compounds in a museum in China Using GC-Orbitrap mass spectrometry

Non-targeted analysis (NTA) was used in identifying volatile organic compounds (VOCs) in a museum in China with the gas chromatograph (GC)-Orbitrap-mass spectrometer (MS). Approximately 230 VOCs were detected, of which 117 were observed at 100% frequency across all sampling sites. Although some were common in indoor environments, most of the detected VOCs were rarely reported in previous studies on museum environments. Some of the detected VOCs were found to be associated with the materials used in furnishings and the chemicals applied in conservation treatment. Spearman's correlation analysis showed that several classes of VOCs were well correlated, suggesting their common sources. Compared with compounds in outdoor air, indoor VOCs had a lower level of unsaturation and more portions of chemically reduced compounds. Hierarchical cluster analysis (HCA) were performed. The results suggested that the sampling adsorbents chosen may have a large impact and that a single type of adsorbent may not be sufficient to cover a wide range of compounds in NTA studies. The MonoTrap adsorbent containing octadecylsilane (ODS) and activated carbon (AC) is suitable for aliphatic polar compounds that contain low levels of oxygen, whereas the MonoTrap ODS and silica gel are good at sampling aliphatic and aromatic hydrocarbons with limited polarity. Principle component analysis (PCA) showed that the indoor VOCs changed significantly at different times in the museum; this may have been caused by the removal of artifacts and refurbishment of the gallery between sampling events. A comparison with compounds identified by chamber emission tests showed that decorative materials may have been one of the main sources of indoor VOCs in the museum. The VOCs identified in the present study are likely to be present in other similar museums; therefore, further examination may be warranted of their potential impacts on cultural heritage artifacts, museum personnel, and visitors.

Molecular insight into the release of phosphate from dissolved organic phosphorus photo-mineralization in shallow lakes based on FT-ICR MS analysis

Dissolved organic phosphorus (DOP) is a key factor in the water eutrophication process because of its high potential bioavailability and inorganic phosphate (Pi) compensation ability through bio- and photo-mineralization. However, the research on the characterization and transformation of DOP is insufficient owing to their complex composition. This study investigates the release of dissolved Pi from DOP photo-mineralization in Lake Dong based on Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) analysis. The results showed that the photo-release of dissolved Pi is spatially heterogeneous in Lake Dong and is consistent with the distribution of DOP concentration. The FT-ICR MS results showed that the simulated irradiation decreased the relative abundance (RA) of the DOP molecular formulae with higher molecular weight (MW) and higher double bond equivalence values (DBE), while the RA of DOP molecular formulae with lower MW and lower DBE value increased or remained. Besides, the total RA of lipid-like formulae increased from 49.09% to 55.90%, while the oxy-aromatic-like formulae decreased from 50.91% to 44.10%, suggesting that simulated irradiation would influence the potential bioavailability of DOP. As the main photolysis medium during DOP photo-mineralization, the hydroxyl radicals (∙OH) are mainly derived from dissolved organic matter (DOM) compared to the nitrate (NO₃^-) and iron ion (Fe³⁺) in Lake Dong. These results are important in understanding the ability and mechanism of DOP photo-mineralization and provide suggestions for cycling phosphorus in eutrophic shallow lakes.

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.

Graph Properties of Mass-Difference Networks for Profiling and Discrimination in Untargeted Metabolomics

Untargeted metabolomics seeks to identify and quantify most metabolites in a biological system. In general, metabolomics results are represented by numerical matrices containing data that represent the intensities of the detected variables. These matrices are subsequently analyzed by methods that seek to extract significant biological information from the data. In mass spectrometry-based metabolomics, if mass is detected with sufficient accuracy, below 1 ppm, it is possible to derive mass-difference networks, which have spectral features as nodes and chemical changes as edges. These networks have previously been used as means to assist formula annotation and to rank the importance of chemical transformations. In this work, we propose a novel role for such networks in untargeted metabolomics data analysis: we demonstrate that their properties as graphs can also be used as signatures for metabolic profiling and class discrimination. For several benchmark examples, we computed six graph properties and we found that the degree profile was consistently the property that allowed for the best performance of several clustering and classification methods, reaching levels that are competitive with the performance using intensity data matrices and traditional pretreatment procedures. Furthermore, we propose two new metrics for the ranking of chemical transformations derived from network properties, which can be applied to sample comparison or clustering. These metrics illustrate how the graph properties of mass-difference networks can highlight the aspects of the information contained in data that are complementary to the information extracted from intensity-based data analysis.

Microbial Interactions in Kombucha through the Lens of Metabolomics

Kombucha is a fermented beverage obtained through the activity of a complex microbial community of yeasts and bacteria. Exo-metabolomes of kombucha microorganisms were analyzed using FT-ICR-MS to investigate their interactions. A simplified set of microorganisms including two yeasts (Brettanomyces bruxellensis and Hanseniaspora valbyensis) and one acetic acid bacterium (Acetobacter indonesiensis) was used to investigate yeast–yeast and yeast–acetic acid bacterium interactions. A yeast–yeast interaction was characterized by the release and consumption of fatty acids and peptides, possibly in relationship to commensalism. A yeast–acetic acid bacterium interaction was different depending on yeast species. With B. bruxellensis, fatty acids and peptides were mainly produced along with consumption of sucrose, fatty acids and polysaccharides. In opposition, the presence of H. valbyensis induced mainly the decrease of polyphenols, peptides, fatty acids, phenolic acids and putative isopropyl malate and phenylpyruvate and few formulae have been produced. With all three microorganisms, the formulae involved with the yeast–yeast interactions were consumed or not produced in the presence of A. indonesiensis. The impact of the yeasts’ presence on A. indonesiensis was consistent regardless of the yeast species with a commensal consumption of compounds associated to the acetic acid bacterium by yeasts. In detail, hydroxystearate from yeasts and dehydroquinate from A. indonesiensis were potentially consumed in all cases of yeast(s)–acetic acid bacterium pairing, highlighting mutualistic behavior.

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.

Inferring the Contribution of Microbial Taxa and Organic Matter Molecular Formulas to Ecological Assembly

Understanding the mechanisms underlying the assembly of communities has long been the goal of many ecological studies. While several studies have evaluated community wide ecological assembly, fewer have focused on investigating the impacts of individual members within a community or assemblage on ecological assembly. Here, we adapted a previous null model β-nearest taxon index (βNTI) to measure the contribution of individual features within an ecological community to overall assembly. This new metric, called feature-level βNTI (βNTI_feat), enables researchers to determine whether ecological features (e.g., individual microbial taxa) contribute to divergence, convergence, or have insignificant impacts across spatiotemporally resolved metacommunities or meta-assemblages. Using βNTI_feat, we revealed that unclassified microbial lineages often contributed to community divergence while diverse groups (e.g., Crenarchaeota, Alphaproteobacteria, and Gammaproteobacteria) contributed to convergence. We also demonstrate that βNTI_feat can be extended to other ecological assemblages such as organic molecules comprising organic matter (OM) pools. OM had more inconsistent trends compared to the microbial community though CHO-containing molecular formulas often contributed to convergence, while nitrogen and phosphorus-containing formulas contributed to both convergence and divergence. A network analysis was used to relate βNTI_feat values from the putatively active microbial community and the OM assemblage and examine potentially common contributions to ecological assembly across different communities/assemblages. This analysis revealed that P-containing formulas often contributed to convergence/divergence separately from other ecological features and N-containing formulas often contributed to assembly in coordination with microorganisms. Additionally, members of Family Geobacteraceae were often observed to contribute to convergence/divergence in conjunction with both N- and P-containing formulas, suggesting a coordinated ecological role for family members and the nitrogen/phosphorus cycle. Overall, we show that βNTI_feat offers opportunities to investigate the community or assemblage members, which shape the phylogenetic or functional landscape, and demonstrate the potential to evaluate potential points of coordination across various community types.

Molecular investigation on changing behaviors of natural organic matter by coagulation with non-targeting screen using high-resolution mass spectrometry

Natural organic matter (NOM) can tremendously influence the purification efficiency of the drinking water treatment process. Coagulation was the first and primary process of NOM removal in the drinking water treatment process. The interaction between coagulants and NOM molecules remains unclear. Three typical coagulants (Al₁₃, FeCl_3, and AlCl₃) were used to investigate the effects on NOM removal. The measurement of NOM was conducted using 15 T Electrospray Ionization coupled Fourier-Transform-Ion Cyclotron Resonance Mass Spectrometry (ESI-FT-ICR MS). The coagulation process altered the mass peak numbers as well as relative intensity of the peaks which were positively correlated with TOC value. The lignin-like compound was the most abundant moiety in raw water. Al-based coagulants remove more unsaturated larger compounds (lower KMD and higher carbon number). Al₁₃ remove the unsaturated hydrocarbons preferably. FeCl₃ is more reactive with NOM molecules and removes more fully saturated compounds. These findings revealed the coagulation removal mechanism of NOM with different structural characteristics and advise the practical use of coagulants for various raw water with different NOM characteristics.

Non-Targeted Metabolomic Analysis of the Kombucha Production Process

Kombucha is a traditional fermented beverage obtained from the transformation of sugared black tea by a community of yeasts and bacteria. Kombucha production recently became industrialized, but its quality standards remain poorly defined. Metabolomic analyses were applied using FT-ICR-MS to characterize the impacts of production phases and the type of tea on the non-volatile chemical composition of kombucha. Independently from tea type, the first phase of acidification in open vessel was characterized by the release of gluconate and gallate from acetic acid bacteria metabolism and probably from polymeric polyphenols, respectively. The second phase of carbonation in closed vessel induced a consumption or transformation of oleic acid that could be consecutive of oxygen limitation. The first phase had the most impact on molecular diversity, but tea type mainly influenced the global composition in polyphenol profile. Black tea polyphenols were more impacted by microbial activity compared to green tea polyphenols.

Enhanced Speciation of Pyrogenic Organic Matter from Wildfires Enabled by 21 T FT-ICR Mass Spectrometry

Wildfires affect soils through the formation of pyrogenic organic matter (pyOM) (e.g., char and soot). While many studies examine the connection between pyOM persistence and carbon (C) composition, nitrogen (N) transformation in wildfire-impacted systems remains poorly understood. Thermal reactions in wildfires transform biomass into a highly complex, polyfunctional, and polydisperse organic mixture that challenges most mass analyzers. High-field Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) is the only mass analyzer that achieves resolving powers sufficient to separate species that differ in mass by the mass of an electron across a wide molecular weight range (m/z 150-1500). We report enhanced speciation of organic N by positive-ion electrospray ionization (ESI) that leverages ultrahigh resolving power (m/Δm_50% = 1 800 000 at m/z 400) and mass accuracy (<10-100 ppb) achieved by FT-ICR MS at 21 T. Isobaric overlaps, roughly the mass of an electron (M_e^- = 548 μDa), are resolved across a wide molecular weight range and are more prevalent in positive ESI than negative ESI. The custom-built 21 T FT-ICR MS instrument identifies previously unresolved mass differences in C_cH_hN_nO_oS_s formulas and assigns more than 30 000 peaks in a pyOM sample. This is the first molecular catalogue of pyOM by positive-ion ESI 21 T FT-ICR MS and presents a method to provide new insight into terrestrial cycling of organic carbon and nitrogen in wildfire impacted ecosystems.

Chemical characterization of dissolved organic matter as disinfection byproduct precursors by UV/fluorescence and ESI FT-ICR MS after smoldering combustion of leaf needles and woody trunks of pine (Pinus jeffreyi)

Forested land plays an essential role in water supply across the United States (US). Smoldering commonly existing in wildfires contributes significantly to biomass consumption and gas emission, but its influence on source water quality has been rarely studied. Here, we investigated the impact of smoldering temperature (i.e., no burn, 250, 400, and 600 °C) on the nutrients, elements, and dissolved organic matter (DOM) of water extracts from the residues of the leaf needles and woody trunks of pine (Pinus jeffreyi) under the lab-simulated smoldering fire. Results showed the increase of pH and the yields of the dominated exchangeable cations of K+ and Mg2+, P, PO43--P, and SO42- with increasing temperature increasing from 250 to 600 °C, whereas significant decreases in the fraction of dissolved organic C in residue C with increasing temperature and the yields of dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) after burnings. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) presented consistent results with UV/fluorescence, suggesting that the unburned materials contained more biodegradable tyrosine/tryptophan/soluble microbial byproduct-like compounds with high molecular weight (MW), whereas the 600 °C-smoldering materials composed of more aromatic, humified, fulvic/humic acid-like, and oxidized compounds with a potentially high density of C=C bonds had less reactivity in forming trihalomethanes (THMs) and haloacetonitriles (HANs). Our study indicates the smoldering-dominated prescribed fire as a potential forest management strategy for reducing biomass fuel and disinfection byproducts (DBPs) precursors in source water from forested lands.