Indexing Permafrost Soil Organic Matter Degradation Using High-Resolution Mass Spectrometry

Old but not ancient: Rock-leached organic carbon drives groundwater microbiomes

More than 90% of earth's microbial biomass resides in the continental subsurface, where sedimentary rocks provide the largest source of organic carbon (C). While many studies indicate microbial utilization of fossil C sources, the extent to which rock-organic C is driving microbial activities in aquifers remains largely unknown. Here we incubated oxic and anoxic groundwater with crushed carbonate rocks from the host aquifer and an outcrop rock of the unsaturated zone characterized by higher organic C content, and compared the natural abundance of radiocarbon (14C) of available C pools and microbial biomarkers. The ancient rocks surprisingly released organic substances with up to 72.6 ± 0.3% modern C into the groundwater, suggesting leachable fresh organic material from surface transport was preserved within rock fractures. Over half of the rock-leached compounds were also found in the original groundwater dissolved organic carbon (DOC), indicating in situ release of material stored in rock fractures through weathering processes. In addition to aliphatic and aromatic hydrocarbons, rock-leachates were rich in lipids, peptides, and carbohydrates. Radiocarbon analysis of phospholipid-derived fatty acids showed a rapid microbial response to this 'younger' organic material, comprising up to 31% (anoxic) and 51% (oxic) of their biomass C from the rock-leachate after 18 days of incubation. Predictive functional profiling of rock-enriched taxa, including species of Desulfosporosinus, Ferribacterium and Rhodoferax, also suggested metabolic potential for aliphatic and aromatic hydrocarbon degradation. PLFAs of the original groundwater were highly 14C-depleted, indicating utilization of a mixture of fossil and 'younger' C sources. Our findings suggest that carbonate rocks act as temporal sink for 'younger' organic matter, that leaches with fossil hydrocarbons from sedimentary rocks, driving microbial metabolism in subsurface ecosystems.

Nitrogen-driven shifts in molecular composition of soil dissolved organic matter linked to rare bacterial sub-communities

The interaction between soil dissolved organic matter (DOM) and bacterial communities is critical for understanding key processes in the global carbon cycle. However, the molecular-level associations between these components remain poorly understood. To address this gap, high-resolution Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was combined with high-throughput sequencing to examine how DOM composition and bacterial sub-community diversity respond to different levels of nitrogen (N) addition (0, 40, and 80 kg N ha-1 yr-1) and to explore the relationships between them. The results demonstrate a significant decline in carbohydrate molecules within DOM under low N conditions. Conversely, the β-diversity and double bond equivalents of DOM molecules increased, indicating greater heterogeneity and stability in DOM composition under this treatment. Rare bacterial sub-communities, as opposed to abundant taxa, were more sensitive to N addition, exhibiting narrower ecological niches and weaker phylogenetic signals. β-Diversity decomposition analysis indicated that compositional differences in abundant taxa were primarily driven by richness differences, whereas those in rare taxa were predominantly influenced by species replacement. Co-occurrence network analysis revealed that DOM molecules were more frequently linked with rare taxa than with abundant taxa. Furthermore, a strong positive relationship was observed between the β-diversity of rare taxa and that of DOM molecules along the N gradient. These findings underscore that rare bacterial sub-communities are the primary drivers of changes in DOM molecular composition under N enrichment, emphasizing their potential role in shaping chemical diversity.

Elucidating the Composition and Transformation of Dissolved Organic Matter at the Sediment-Water Interface Using High-Resolution Mass Spectrometry

The exchange and transformation of dissolved organic matter (DOM) at the sediment-water interface are crucial factors in regulating watershed biogeochemistry, with the molecular composition of DOM serving as a pivotal determinant in elucidating this process. High-resolution mass spectrometry (HRMS) is an effective tool for resolving the composition of DOM. By analyzing the compositional characteristics of DOM at the sediment-water interface under three different salinities at the same latitude region in northern China, the findings indicate certain variations in component characteristics of DOM between low-salinity inland waters and high-salinity seawaters, with the former exhibiting greater molecular diversity and higher molecular weights, whereas the latter displayed a higher saturation and bioavailability. Notably, the presence of more CHOS substances in the low-salinity inland waters underscores the transformation of the DOM influenced by terrestrial inputs and anthropogenic activities. Conversely, the presence of more CHO and CHNO substances in high-salinity seawater underscores the microbial effects. The chemical transformation process from overlying water to pore water to sediments was characterized by methylation, hydrogenation, decarboxylation, and reduction, as determined by calculating the relations between the H/C and O/C ratios of different compound types. These findings indicate that HRMS can yield more refined results in revealing the process of DOM at the sediment-water interface under different environments, which provides a more reliable basis for a deeper understanding of the source-sink mechanism of sediment organic matter.

High-Resolution Tandem Mass Spectrometry-Based Analysis of Model Lignin-Iron Complexes: Novel Pipeline and Complex Structures

Understanding the chemical nature of soil organic carbon (SOC) with great potential to bind iron (Fe) minerals is critical for predicting the stability of SOC. Organic ligands of Fe are among the top candidates for SOCs able to strongly sorb on Fe minerals, but most of them are still molecularly uncharacterized. To shed insights into the chemical nature of organic ligands in soil and their fate, this study developed a protocol for identifying organic ligands using ultrahigh-performance liquid chromatography-high-resolution tandem mass spectrometry (UHPLC-HRMS/MS) and metabolomic tools. The protocol was used for investigating the Fe complexes formed by model compounds of lignin-derived organic ligands, namely, caffeic acid (CA), p-coumaric acid (CMA), vanillin (VNL), and cinnamic acid (CNA). Isotopologue analysis of 54/56Fe was used to screen out the potential UHPLC-HRMS (m/z) features for complexes formed between organic ligands and Fe, with multiple features captured for CA, CMA, VNL, and CNA when 35/37Cl isotopologue analysis was used as supplementary evidence for the complexes with Cl. MS/MS spectra, fragment analysis, and structure prediction with SIRIUS were used to annotate the structures of mono/bidentate mono/biligand complexes. The analysis determined the structures of monodentate and bidentate complexes of FeLxCly (L: organic ligand, x = 1-4, y = 0-3) formed by model compounds. The protocol developed in this study can be used to identify unknown organic ligands occurring in complex environmental samples and shed light on the molecular-level processes governing the stability of the SOC.

Changes in coal waste DOM chemodiversity and Fe/Al oxides during weathering drive the fraction conversion of heavy metals

The long-term accumulation of coal waste on the surface during natural weathering leads to the inevitable migration of heavy metals contained in the coal waste, which increases the likelihood of environmental contamination and health risks. Dissolved organic matter (DOM) and Fe/Al oxides play crucial roles in the transformation and bioavailability of heavy metals. Thus, we analyzed the Fe/Al oxide content and DOM molecular composition in coal waste with different degrees of weathering and explored the influence of DOM chemical diversity and Fe/Al oxides on the potential mobility of heavy metals. Results showed that weathering-driven decrease in Fe oxides (Fed, FeO, and Fep decreased from 82.4, 37.5, and 3.6 mg∙L-1 to 41.3, 24.7, and 2.3 mg∙L-1, respectively) led to decreases in the reducible fractions of V and Cr. The potential environmental risks of more toxic metals of Cd and As, also increased as a result of the residual fractions decreased to 32.6 % and 41.3 %, respectively. Weathering caused an increase in oxygen-to‑carbon ratio, double-bond equivalent, modified aromaticity index, nominal oxidation state of carbon, and molecular diversity and a decrease in (m/z)w and (H/C)w, suggesting that the DOM of highly weathered coal waste possessed high unsaturation, aromatic structures, hydrophilicity, and strong oxidative characteristics. Additionally, although VMF and CrMF showed significant negative correlations with O/C ratio, polyphenolic, carbohydrates, and condensed aromatics, pH remained a key environmental factor determining the potential environmental risks of V and Cr by changing the residual fractions. The mobilities of Cd and As were significantly negatively correlated with those of Fe/Al oxides, particularly Fed, FeO, Fep, and Alp. Our findings contribute to the understanding of the impact of weathering on the geochemical cycling of different coal waste components, providing priority options for environmental risk prevention and control in coal mining areas.

Spatial heterogeneity and compositional profiles of dissolved organic matter in farmland soils across mainland China

Dissolved organic matter (DOM) plays an essential role in many geochemical processes, however its complexity, chemical diversity, and molecular composition are poorly understood. Soil samples were collected from 500 vegetable fields in administrative regions of mainland China, of which 122 were selected for further investigation. DOM properties were characterized by three-dimensional excitation-emission matrix (3D-EEM) fluorescence spectroscopy and Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) (field intensity is 15 Tesla). Our results indicated that the main constituents were UVA humic-like substances, humic-like substances, fulvic acid-like substances, and tyrosine-like substances. A total of 10,989 molecular formulae with a mass range of 100.04 to 799.59 Da were detected, covering the mass spectrometric information of the soil samples from 27 different regions. CHO and CHON molecules were dominant in DOM, whereas lignin, tannins, and aromatic substances served as the main components. The results of cluster analysis revealed that the soil properties in Jiangxi Province were considerably different from those in other regions. The key backgrounds of the DOM molecular characteristics in the vegetable-field soil samples across mainland China were provided at the molecular level, with large abundance and great variability.

Database and review of disinfection by-products since 1974: Constituent elements, molecular weights, and structures

Since trihalomethanes were discovered in 1974, disinfection by-products (DBPs) in drinking water have attracted extensive attention. In 2011, more than 600 known DBPs were compiled; however, newly reported DBPs have not been integrated. The rapid development of mass spectrometry has led to a significant increase in the number of DBPs, therefore, there is a need to develop a database of all DBPs and their properties. Herein, a database including 6310 DBPs (651 confirmed, 1478 identified and 4142 proposed) reported between 1974 and 2022 was constructed and made available for public use at https://dbps.com.cn/main. This database can be a tool in screening new DBPs, comprehensively reviewing, and developing predictive models. In this paper, to demonstrate the functions of the database and provide useful information for this area, the origin of the collected DBPs was presented, and some basic information, including elemental composition, molecular weight, functional groups, and carbon frameworks, were comparatively analyzed. The results showed that the proportion of DBPs verified by standard compounds and frequently detected in real water is less than 7.0%, and most of DBPs remained to be identified. Approximately 88% of DBPs contain halogens, and brominated -DBPs occupied a similar ratio to chlorinated -DBPs in real water. Acids were the main functional groups of DBPs, aliphatic and aromatic compounds are the two major carbon frameworks, and the molecular weights of most DBPs ranged from 200 to 400 Da. In addition, 4142 proposed DBPs as obtained using high-resolution mass spectrometry, were characterized based on the modified van Krevelen diagram and adjusted indexes with halogens. Most of the proposed DBPs featured lignin and tannin structures, and phenolic/highly unsaturated DBPs account for the majority.

High Voltage: The Molecular Properties of Redox-Active Dissolved Organic Matter in Northern High-Latitude Lakes

Redox-active functional groups in dissolved organic matter (DOM) are crucial for microbial electron transfer and methane emissions. However, the extent of aquatic DOM redox properties across northern high-latitude lakes and their relationships with DOM composition have not been thoroughly described. We quantified electron donating capacity (EDC) and electron accepting capacity (EAC) in lake DOM from Canada to Alaska and assessed their relationships with parameters from absorbance, fluorescence, and ultrahigh resolution mass spectrometry (FT-ICR MS) analyses. EDC and EAC are strongly tied to aromaticity and negatively related to aliphaticity and protein-like content. Redox-active formulae spanned a range of aromaticity, including highly unsaturated phenolic formulae, and correlated negatively with many aliphatic N and S-containing formulae. This distribution illustrates the compositional diversity of redox-sensitive functional groups and their sensitivity to ecosystem properties such as local hydrology and residence time. Finally, we developed a reducing index (RI) to predict EDC in aquatic DOM from FT-ICR MS spectra and assessed its robustness using riverine DOM. As the hydrology of the northern high-latitudes continues to change, we expect differences in the quantity and partitioning of EDC and EAC within these lakes, which have implications for local water quality and methane emissions.

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.

Chemodiversity of dissolved organic matter in cadmium-contaminated paddy soil amended with different materials

Dissolved organic matter (DOM) in soil is a key factor affecting the bioavailability of heavy metals, but very few studies have focused on the role of DOM in the use of soil amendments to mitigate heavy metal accumulation in crops. Here, eleven materials were added to cadmium (Cd)-contaminated paddy soil in greenhouse pot trials; rice was grown and harvested, the chemodiversity of post-harvest soil DOM was characterized using Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry, and the specific associations between soil DOM traits and water-extractable soil Cd concentration were identified at the molecular level. The results showed that the endogenous release caused by altering soil pH had a greater effect on soil DOM concentration than did the exogenous chemical input due to the application of organic amendments, which in turn contributed to the chemodiversity of DOM. After one season of rice cultivation, soil DOM molecules were mainly dominated by relatively low molecular weight heteroatom-free lignins. C/N, C/H ratios of organic materials influenced DOM molecular fingerprint patterns, and soil pH and redox potential were the main driving forces affecting the chemodiversity of DOM. Furthermore, the low molecular weight, high saturation, low aromaticity, and heteroatom-free DOM molecules are more likely to dissolve Cd from the soil solid phase, thus increasing the potential risk of Cd to the environment. The results provide critical information about amendments-induced changes in DOM chemodiversity and will inform the selection of appropriate soil amendments.

Molecular compositions, optical properties, and implications of dissolved brown carbon in snow/ice on the Tibetan Plateau glaciers

Brown carbon (BrC)/water-soluble organic carbon (WSOC) plays a crucial role in glacier melting. A quantitative evaluation of the light absorption characteristics of WSOC on glacier melting is urgently needed, as the WSOC release from glaciers potentially affects the hydrological cycle, downstream ecological balance, and the global carbon cycle. In this work, the optical properties and composition of WSOC in surface snow/ice on four Tibetan Plateau (TP) glaciers were investigated using a three-dimensional fluorescence spectrometer and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. The total light-absorption of WSOC in snow/ice at 250-400 nm (ultraviolet region) and 400-600 nm (visible region) accounted for about 60.42% and 27.17% of the light absorption by the total organics, respectively. Two protein-like substances (PRLIS), one humic-like substance (HULIS), and one undefined species of chromophores in snow/ice on the TP glacier surfaces were identified. The lignins and lipids were the main compounds in the TP glaciers and were presented as CHO and CHNO molecules, while CHNOS molecules were only observed in the southeast TP glacier. The light absorption capacity of WSOC in snow/ice was mainly affected by their oxidizing properties. PRLIS and undefined species were closely linked to microbial sources and the local environment of the glaciers (lignins and lipids), while HULIS was significantly affected by anthropogenic emissions (protein/amino sugars). Radiative forcing (RF)-induced by WSOC relative to black carbon were accounted for about 11.62 ± 12.07% and 8.40 ± 10.37% in surface snow and granular ice, respectively. The RF was estimated to be 1.14 and 6.36 W m^-2 in surface snow and granular ice, respectively, during the melt season in the central TP glacier. These findings contribute to our understanding of WSOC's impact on glaciers and could serve as a baseline for WSOC research in cryospheric science.

Relation between lignin molecular profile and fungal exo-proteome during kraft lignin modification by Trametes hirsuta LE-BIN 072

The process of kraft lignin modification by the white-rot fungus Trametes hirsuta was investigated using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS), and groups of systematically changing compounds were delineated. In the course of cultivation, fungus tended to degrade progressively more reduced compounds and produced more oxidized ones. However, this process was not gradual - the substantial discontinuity was observed between 6th and 10th days of cultivation. Simultaneously, the secretion of ligninolytic peroxidases by the fungus was changing in a cascade manner - new isoenzymes were added to the mixture of the already secreted ones, and once new isoenzyme appeared both its relative quantity and number of isoforms increased as cultivation proceeded. It was proposed, that the later secreted peroxidases (MnP7 and MnP1) possess higher substrate affinity for some phenolic compounds and act in more specialized manner than the early secreted ones (MnP5 and VP2).

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

The biogeochemical cycling of soil organic matter (SOM) plays a central role in regulating soil health, water quality, carbon storage, and greenhouse gas emissions. Thus, many studies have been conducted to reveal how anthropogenic and climate variables affect carbon sequestration and nutrient cycling. Among the analytical techniques used to better understand the speciation and transformation of SOM, Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) is the only technique that has sufficient mass resolving power to separate and accurately assign elemental compositions to individual SOM molecules. The global increase in the application of FTICR MS to address SOM complexity has highlighted the many challenges and opportunities associated with SOM sample preparation, FTICR MS analysis, and mass spectral interpretation. Here, we provide a critical review of recent strategies for SOM characterization by FTICR MS with emphasis on SOM sample collection, preparation, analysis, and data interpretation. Data processing and visualization methods are presented with suggested workflows that detail the considerations needed for the application of molecular information derived from FTICR MS. Finally, we highlight current research gaps, biases, and future directions needed to improve our understanding of organic matter chemistry and cycling within terrestrial ecosystems.

Biofilm development of Bacillus siamensis ATKU1 on pristine short chain low-density polyethylene: A case study on microbe-microplastics interaction

A low-density polyethylene (LDPE) degrading bacterial strain (ATKU1) was isolated (99.86% similar with Bacillus siamensis KCTC 13613^T) from a plastic dumping site to study interactions between microplastics (< 5 mm) and microorganisms. The strain was found (by scanning electron microscopy) to form biofilm on the microplastic surface after its interaction with LDPE (avg. M_w~4,000 Da and avg. M_n~1,700 Da) as a sole carbon source. Atomic force microscopy (AFM) showed the biofilm's 3-D developmental patterns and significantly increased Young's modulus of the LDPE surface after microbial treatment. Most of the viable bacteria attached to biofilms rather than media, which suggested their ability to utilize LDPE. Absorption bands of carbonyl, alkenyl, acyl, ester, primary-secondary alcohol, alkene groups and nitric oxides were found on the treated LDPE particles using Fourier-transform infrared spectroscopy. Fourier transform-ion cyclotron resonance mass spectrometry of the media indicated compositional shifts of the compounds after treatment (i.e., increase in the degree of unsaturation and increment in oxygen-to-carbon ratio) and presence of unsaturated hydrocarbons, polyketides, terpenoids, aliphatic/peptides, dicarboxylic acids, lipid-like compounds were hinted. The plastic degrading abilities of Bacillus siamensis ATKU1 suggest its probable application for large scale plastic bioremediation facility.

Characteristics and Evolution of Nitrogen in the Heavy Components of Algae Pyrolysis Bio-Oil

Algae pyrolytic bio-oil contains a large quantity of N-containing components (NCCs), which can be processed as valuable chemicals, while the harmful gases can also be released during bio-oil upgrading. However, the characteristics of NCCs in the bio-oil, especially the composition of heavy NCCs (molecular weight ≥200 Da), have not been fully studied due to the limitation of advanced analytical methods. In this study, three kinds of algae rich in lipids, proteins, and carbohydrates were rapidly pyrolyzed (10-25 °C/s) at different temperatures (300-700 °C). The bio-oil was analyzed using a Fourier transform ion cyclotron resonance mass spectrometer equipped with electrospray ionization, and the characteristics and evolution of nitrogen in heavy components were first obtained. The results indicated that the molecular weight of most heavy NCCs was distributed in the 200-400 Da range. N_1-3 compounds account for over 60% in lipid and protein-rich samples, while N₀ and N₄ components are prominent in carbohydrate-rich samples. As temperature increases, most NCCs become more aromatic and contain less O due to the strong Maillard and deoxygenation reactions. Moreover, the heavier NCCs were promoted to form lighter compounds with more nitrogen atoms through decomposition (mainly denitrogenation and deoxygenation). Finally, some strategies to deal with the NCCs for high-quality bio-oil production were proposed.

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

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

Untargeted Exometabolomics Provides a Powerful Approach to Investigate Biogeochemical Hotspots with Vegetation and Polygon Type in Arctic Tundra Soils

Rising temperatures in the Arctic have led to the thawing of tundra soils, which is rapidly changing terrain, hydrology, and plant and microbial communities, causing hotspots of biogeochemical activity across the landscape. Despite this, little is known about how nutrient-rich low molecular weight dissolved organic matter (LMW DOM) varies within and across tundra ecosystems. Using a high-resolution nano-liquid chromatography-mass spectrometry (LC/MS) approach, we characterized the composition and availability of LMW DOM from high-centered polygons (HCP) and low-centered polygons (LCP) with Eriophorum angustifolium or Carex aquatilis as the dominant vegetation. Over 3000 unique features (i.e., discrete mass/charge ions) were detected; 521 were identified as differentially abundant between polygonal types and 217 were putatively annotated using high mass accuracy MS data. While polygon type was a strong predictor of LMW DOM composition and availability, vegetation and soil depth were also important drivers. Extensive evidence was found for enhanced microbial processing at the LCP sites, which were dominated by Carex plant species. We detected significant differences between polygon types with varying aboveground landscape features or properties, and hotspots of biogeochemical activity, indicating LMW DOM, as quantified by untargeted exometabolomics, provides a window into the dynamic complex interactions between landscape topography, vegetation, and organic matter cycling in Arctic polygonal tundra soils.

Comparison of the chemical diversity of Vitis rotundifolia and Vitis vinifera cv. ‘Cabernet Sauvignon’

Grapevine is one of the most important fruit plants in the world, mainly due to its grapes and related products, with a highly economic and cultural importance. Every year, vineyards are affected by several pathogen outbreaks and the only way to control them is through preventive applications of agrochemicals every 12 to 15 days. This approach is not sustainable and not always effective. The Vitis genus comprise different species that exhibit varying levels of resistance to pathogens, thus the understanding of the innate resistance/susceptibility mechanisms of these different Vitis species is crucial to cope with these threats. In this work, an untargeted metabolomics approach was followed, using Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR-MS), to analyse the metabolic chemical diversity of two Vitis species: Vitis rotundifolia (resistant to pathogens) and V. vinifera cv. ‘Cabernet Sauvignon’ (susceptible to pathogens). Chemical formulas from both Vitis were used to build Van Krevelen diagrams and compositional space plots, which do not require full metabolite identification and provide an easy comparison method. Based only on these visualization tools, it was shown that the V. rotundifolia metabolome is more complex than the metabolome of V. vinifera cv. ‘Cabernet Sauvignon’. Moreover, the regions that present a higher density are associated to lipids, polyketides and carbohydrates. Also, V. rotundifolia metabolome presented a higher ratio O/C compounds.

Deciphering Dissolved Organic Matter: Ionization, Dopant, and Fragmentation Insights via Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry

Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) has been increasingly employed to characterize dissolved organic matter (DOM) across a range of aquatic environments highlighting the role of DOM in global carbon cycling. DOM analysis commonly utilizes electrospray ionization (ESI), while some have implemented other techniques, including dopant-assisted atmospheric pressure photoionization (APPI). We compared various extracted DOM compositions analyzed by negative ESI and positive APPI doped with both toluene and tetrahydrofuran (THF), including a fragmentation study of THF-doped riverine DOM using infrared multiple photon dissociation (IRMPD). DOM compositions followed the same trends in ESI and dopant-assisted APPI with the latter presenting saturated, less oxygenated, and more N-containing compounds than ESI. Between the APPI dopants, THF-doping yielded spectra with more aliphatic-like and N-containing compounds than toluene-doping. We further demonstrate how fragmentation of THF-doped DOM in APPI resolved subtle differences between riverine DOM that was absent from ESI. In both ionization methods, we describe a linear relationship between atomic and formulaic N-compositions from a range of DOM extracts. This study highlights that THF-doped APPI is useful for uncovering low-intensity aliphatic and peptide-like components in autochthonous DOM, which could aid environmental assessments of DOM across biolability gradients.

Application of Fourier transform ion cyclotron resonance mass spectrometry to characterize natural organic matter

Advances in the ultra-high-resolution mass spectroscopy lead to a deep insight into the molecular characterization of natural organic matter (NOM). Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) has been used as one of the most powerful tools to decipher NOM molecules. In FTICR-MS analysis, the matrix effects caused by the co-occurring inorganic substances in water samples greatly affect the ionization of NOM molecules. The inherent complexity of NOM may hinder its component classification and formula assignment. In this study, basic principles and recent advances for sample separation and purification approaches, ionization methods, and the evolutions in formula assignment and data exploitation of the FTICR-MS analysis were reviewed. The complementary characterization methods for FTICR-MS were also reviewed. By coupling with other developed/developing characterization methods, the statistical confidence for inferring the NOM compositions by FTICR-MS was greatly improved. Despite that the refined separation procedures and advanced data processing methods for NOM molecules have been exploited, the big challenge for interpreting NOM molecules is to give the basic structures of them. Online share of the FTICR-MS data, further optimizing the FTICR-MS technique, and coupling this technique with more characterization methods would be beneficial to improving the understanding of the composition and property of NOM.

Linking molecular and optical properties of dissolved organic matter across a soil-water interface on Akimiski Island (Nunavut, Canada)

Dissolved organic matter (DOM) plays a crucial role in terrestrial and aquatic carbon and biogeochemical cycles; however, molecular transformations between aquatic and terrestrial systems remain poorly understood due to the complexity and heterogeneity of DOM. In this study, we investigated the molecular diversity of aquatic DOM and adjacent soil derived water extractable organic matter (WEOM) from seven locations on Akimiski Island, Nunavut using a combination of absorbance spectroscopy and Fourier transform ion cyclotron mass spectrometry (FT-ICR-MS). Assigned elemental formula and Van Krevelen compositional analysis reveal compositional similarities in river, inland ponds and coastal pool sites for aquatic DOM and WEOM. More aromatic, oxygenated polyphenolic carbon rich molecules were found in aquatic DOM whereas WEOM was abundant in highly unsaturated aliphatic material. A total of 276 phenolic, unsaturated aliphatic, and vascular plant-derived polyphenolic molecules were identified as being conserved between WEOM and aquatic DOM at one river and two inland pond locations suggesting similar CHO sources from adjacent soils. Moreover, contributions of polyphenolic compounds in aquatic DOM and WEOM were greater at inland ponds than coastal pools, congruent with a greater aromaticity at inland sites. Our results highlight the similarities and differences in WEOM to aquatic DOM composition and how they range across surrounding watersheds that provide insight into the biogeochemical dynamics across a Canadian subarctic terrestrial-aquatic-continuum.

Generic parameters of first-order kinetics accurately describe soil organic matter decay in bare fallow soils over a wide edaphic and climatic range

The conventional soil organic matter (SOM) decay paradigm considers the intrinsic quality of SOM as the dominant decay limitation with the result that it is modelled using simple first-order decay kinetics. This view and modelling approach is often criticized for being too simplistic and unreliable for predictive purposes. It is still under debate if first-order models can correctly capture the variability in temporal SOM decay observed between different agroecosystems and climates. To address this question, we calibrated a first-order model (Q) on six long-term bare fallow field experiments across Europe. Following conventional SOM decay theory, we assumed that parameters directly describing SOC decay (rate of SOM quality change and decomposer metabolism) are thermodynamically constrained and therefore valid for all sites. Initial litter input quality and edaphic interactions (both local by definition) and microbial efficiency (possibly affected by nutrient stoichiometry) were instead considered site-specific. Initial litter input quality explained most observed kinetics variability, and the model predicted a convergence toward a common kinetics over time. Site-specific variables played no detectable role. The decay of decades-old SOM seemed mostly influenced by OM chemistry and was well described by first order kinetics and a single set of general kinetics parameters.

Electrochemical characterization of natural organic matter by direct voltammetry in an aprotic solvent

The complex and indeterminant composition of NOM makes characterization of its redox properties challenging. Approaches that have been taken to address this challenge include chemical probe reactions, potentiometric titrations, chronocoulometry, and voltammetry. In this study, we revisit the use of direct voltammetric methods in aprotic solvents by applying an expanded and refined suite of methods to a large set of NOM samples and model compounds (54 NOM samples from 10 different sources, 7 NOM model compounds, and 2 fresh extracts of plant materials that are high in redox-active quinonoid model compounds dissolved in DMSO). Refinements in the methods of fitting the data obtained by staircase cyclic voltammetry (SCV) provided improved definition of peaks, and square wave voltammetry (SWV), performed under the same conditions as SCV, provided even more reliable identification and quantitation of peaks. Further evidence is provided that DMSO improves the electrode response by unfolding some of the tertiary structure of NOM polymers, thereby allowing greater contact between redox active functional groups and the electrode surface. We averaged experimental peak potentials for all NOM compounds and calculated potentials in water. Average values for Epa1, Epc1, and Ep1 in DMSO were -0.866 ± 0.069, -1.35 ± 0.071, and -0.831 ± 0.051 V vs. Ag/Ag+, and -0.128, -0.613, and -0.0930 V vs. SHE in water. In addition to peak potentials, the breadth of SCV peaks was quantified as a way to characterize the degree to which the redox activity of NOM is due to a continuum of contributing functional groups. The average breadth values were 1.63 ± 0.24, 1.28 ± 0.34, and 0.648 ± 0.15 V for Epa1, Epc1, and Ep1 respectively. Comparative analysis of the overall dataset-from SCV and SWV on all NOMs and model compounds-revealed that NOM redox properties vary over a narrower range than expected based on model compound properties. This lack of diversity in redox properties of NOM is similar to conclusions from other recent work on the molecular structure of NOM, all of which could be the result of selectivity in the common extraction methods used to obtain the materials.

Effect of endogenous microbiota on the molecular composition of cloud water: a study by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS)

A cloud water sample collected at the puy de Dôme observatory (PUY) has been incubated under dark conditions, with its endogenous microbiota at two different temperatures (5 and 15 °C), and the change in the molecular organic composition of this sample was analyzed by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Microorganisms were metabolically active and strongly modified the dissolved organic matter since they were able to form and consume many compounds. Using Venn diagrams, four fractions of compounds were identified: (1) compounds consumed by microbial activity; (2) compounds not transformed during incubation; (3) compounds resulting from dark chemistry (i.e., hydrolysis and Fenton reactions) and, finally, (4) compounds resulting from microbial metabolic activity. At 15 °C, microorganisms were able to consume 58% of the compounds initially present and produce 266 new compounds. For this cloud sample, the impact of dark chemistry was negligible. Decreasing the temperature to 5 °C led to the more efficient degradation of organic compounds (1716 compounds vs. 1094 at 15 °C) but with the less important production of new ones (173). These transformations were analyzed using a division into classes based on the O/C and H/C ratios: lipid-like compounds, aliphatic/peptide-like compounds, carboxylic-rich alicyclic molecule (CRAM)-like structures, carbohydrate-like compounds, unsaturated hydrocarbons, aromatic structures and highly oxygenated compounds (HOCs). Lipid-like, aliphatic/peptide-like and CRAMs-like compounds were the most impacted since they were consumed to maintain the microbial metabolism. On the contrary, the relative percentages of CRAMs and carbohydrates increased after incubation.

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

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

Microbial Interactions With Dissolved Organic Matter Drive Carbon Dynamics and Community Succession

Knowledge of dynamic interactions between natural organic matter (NOM) and microbial communities is critical not only to delineate the routes of NOM degradation/transformation and carbon (C) fluxes, but also to understand microbial community evolution and succession in ecosystems. Yet, these processes in subsurface environments are usually studied independently, and a comprehensive view has been elusive thus far. In this study, we fed sediment-derived dissolved organic matter (DOM) to groundwater microbes and continually analyzed microbial transformation of DOM over a 50-day incubation. To document fine-scale changes in DOM chemistry, we applied high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and soft X-ray absorption spectroscopy (sXAS). We also monitored the trajectory of microbial biomass, community structure and activity over this time period. Together, these analyses provided an unprecedented comprehensive view of interactions between sediment-derived DOM and indigenous subsurface groundwater microbes. Microbial decomposition of labile C in DOM was immediately evident from biomass increase and total organic carbon (TOC) decrease. The change of microbial composition was closely related to DOM turnover: microbial community in early stages of incubation was influenced by relatively labile tannin- and protein-like compounds; while in later stages the community composition evolved to be most correlated with less labile lipid- and lignin-like compounds. These changes in microbial community structure and function, coupled with the contribution of microbial products to DOM pool affected the further transformation of DOM, culminating in stark changes to DOM composition over time. Our study demonstrates a distinct response of microbial communities to biotransformation of DOM, which improves our understanding of coupled interactions between sediment-derived DOM, microbial processes, and community structure in subsurface groundwater.

Molecular Insights into Arctic Soil Organic Matter Degradation under Warming

Molecular composition of the Arctic soil organic carbon (SOC) and its susceptibility to microbial degradation are uncertain due to heterogeneity and unknown SOC compositions. Using ultrahigh-resolution mass spectrometry, we determined the susceptibility and compositional changes of extractable dissolved organic matter (EDOM) in an anoxic warming incubation experiment (up to 122 days) with a tundra soil from Alaska (United States). EDOM was extracted with 10 mM NH₄HCO₃ from both the organic- and mineral-layer soils during incubation at both -2 and 8 °C. Based on their O:C and H:C ratios, EDOM molecular formulas were qualitatively grouped into nine biochemical classes of compounds, among which lignin-like compounds dominated both the organic and the mineral soils and were the most stable, whereas amino sugars, peptides, and carbohydrate-like compounds were the most biologically labile. These results corresponded with shifts in EDOM elemental composition in which the ratios of O:C and N:C decreased, while the average C content in EDOM, molecular mass, and aromaticity increased after 122 days of incubation. This research demonstrates that certain EDOM components, such as amino sugars, peptides, and carbohydrate-like compounds, are disproportionately more susceptible to microbial degradation than others in the soil, and these results should be considered in SOC degradation models to improve predictions of Arctic climate feedbacks.

Van Krevelen diagram visualization of high resolution-mass spectrometry metabolomics data with OpenVanKrevelen

INTRODUCTION

Van Krevelen (VK) diagrams provide a promising but uncommon solution to a number of challenges associated with the visualization of metabolomics data. VK diagrams are created by plotting H:C ratios against O:C ratios of the compounds in a chemical mixture.

OBJECTIVES

The aim of this manuscript is to present an open-source software tool and reference map that we have developed to make VK diagrams for visualization of metabolomics data.

METHODS

Software was created with a prompt-driven command line user interface and was written using Python 2.7. We empirically derived an accompanying map by plotting where compounds from seven biomolecule types fall within the VK plot space.

RESULTS

We've created an easy to use, open source software tool named OpenVanKrevelen for making a range of VK diagrams that is available on GitHub: https://github.com/HegemanLab/VanKrevelenLocal . The empirical mapping approach has produced several improvements from previously published maps.

CONCLUSIONS

OpenVanKrevelen provides the metabolomics community with access to a new tool for visualization of complex metabolomics datasets.

Redox Conditions Affect Dissolved Organic Carbon Quality in Stratified Freshwaters

The quality of dissolved organic carbon (DOC) affects both carbon cycling in surface waters and drinking water production. Not much is known about the influence of environmental conditions on DOC quality. We studied the effect of redox conditions on the chemical composition of DOC in a drinking water reservoir by Fourier transform ion cyclotron resonance mass spectrometry in combination with sediment core incubation experiments under manipulated redox conditions. We observed clear differences in DOC quality among oxic epilimnion, anoxic hypolimnion, and sediment porewater. Sediment porewater showed relatively high intensities of polyphenol-like components with H/C ratios of <1 and O/C ratios of >0.6. Consistent with this, anoxic incubation of a sediment core resulted in an accumulation of these components in the overlying water. The observed pattern of DOC quality change can be explained by redox-dependent adsorption/desorption of DOC on iron minerals. Under oxic conditions, the polyphenol-like components bind on freshly formed iron hydroxides, a process that affects both DOC stability in surface waters and treatability during drinking water production.

Photochemical alteration of organic carbon draining permafrost soils shifts microbial metabolic pathways and stimulates respiration

In sunlit waters, photochemical alteration of dissolved organic carbon (DOC) impacts the microbial respiration of DOC to CO₂. This coupled photochemical and biological degradation of DOC is especially critical for carbon budgets in the Arctic, where thawing permafrost soils increase opportunities for DOC oxidation to CO₂ in surface waters, thereby reinforcing global warming. Here we show how and why sunlight exposure impacts microbial respiration of DOC draining permafrost soils. Sunlight significantly increases or decreases microbial respiration of DOC depending on whether photo-alteration produces or removes molecules that native microbial communities used prior to light exposure. Using high-resolution chemical and microbial approaches, we show that rates of DOC processing by microbes are likely governed by a combination of the abundance and lability of DOC exported from land to water and produced by photochemical processes, and the capacity and timescale that microbial communities have to adapt to metabolize photo-altered DOC.

The role of dissolved organic carbon (DOC) photo-alteration in the microbial respiration of DOC to CO₂ is unclear. Here, the authors show that the impact of this mechanism depends on whether photo-alteration of DOC produces or removes molecules used by native microbial communities prior to light exposure.

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

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

Chemical Composition of Microbe-Derived Dissolved Organic Matter in Cryoconite in Tibetan Plateau Glaciers: Insights from Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Analysis

Cryoconite in mountain glaciers plays important roles in glacial ablation and biogeochemical cycles. In this study, the composition and sources of dissolved organic matter (DOM) in cryoconite from the ablation regions of two Tibetan Plateau glaciers were determined using electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and fluorescence spectrometry. A marked absorbance between 300 and 350 nm in the DOM absorption spectra was observed which was consistent with microbe-derived mycosporine-like amino acids. Fluorescence excitation-emission matrices showed that DOM had intense signals at protein-like substance peaks and weak signals at humic-like substance peaks. The high-resolution mass spectra of FT-ICR-MS showed cryoconite DOM from both glaciers contained diverse lignins, lipids, proteins, and unsaturated hydrocarbons. The lipids and proteins were consistent with material from microbial sources, and the lignins and unsaturated hydrocarbons were probably from vascular plant material supplied in atmospheric aerosols and debris from around the glaciers. Almost one-third of the identified DOM molecules had low C/N ratios (≤20), indicating their high bioavailability. Using a conservative cryoconite distribution on Chinese mountain glacier surfaces (6%) and an average debris mass per square meter of cryoconite (292 ± 196 g m^-2), we found that the amount of DOC produced in cryoconite on Chinese glaciers as much as 0.23 ± 0.1 Gg per cryoconite formation process. This dissolved organic carbon may absorb solar radiation, accelerate glacial melting, and be an important source of bioavailable DOM to proglacial and downstream aquatic ecosystems.

Enhanced Mass Defect Filtering To Simplify and Classify Complex Mixtures of Lignin Degradation Products

High resolution mass spectrometry was utilized to study the highly complex product mixtures resulting from electrochemical breakdown of lignin. As most of the chemical structures of the degradation products were unknown, enhanced mass defect filtering techniques were implemented to simplify the characterization of the mixtures. It was shown that the implemented ionization techniques had a major impact on the range of detectable breakdown products, with atmospheric pressure photoionization in negative ionization mode providing the widest coverage in our experiments. Different modified Kendrick mass plots were used as a basis for mass defect filtering, where Kendrick mass defect and the mass defect of the lignin-specific guaiacol (C7H7O2) monomeric unit were utilized, readily allowing class assignments independent of the oligomeric state of the product. The enhanced mass defect filtering strategy therefore provided rapid characterization of the sample composition. In addition, the structural similarities between the compounds within a degradation sequence were determined by comparison to a tentatively identified product of this compound series. In general, our analyses revealed that primarily breakdown products with low oxygen content were formed under electrochemical conditions using protic ionic liquids as solvent for lignin.