Spatial variations in the molecular diversity of dissolved organic matter in water moving through a boreal forest in eastern Finland

The molecular diversity of dissolved organic matter in forest streams across central Canadian boreal watersheds

Small headwater streams can mobilize large amounts of terrestrially derived dissolved organic matter (DOM). While the molecular composition of DOM has important controls on biogeochemical cycles and carbon cycling, how stationary landscape metrics affect DOM composition is poorly understood, particularly in relation to non-stationary effects from hydrological changes across seasons. Here, we apply a combination of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and absorbance spectroscopy to characterize stream DOM from 13 diverse watersheds across the central Canadian boreal forests and statistically relate DOM compositional characteristics to landscape topography and hydrological metrics. We found that watershed runoff across different surface physiographies produced DOM with distinctly different chemical compositions related to runoff pH. Specifically, streams in sandy soil watersheds contained more abundant aromatic, nitrogenated and sulfurized fractions of DOM, likely due to a combination of lower soil capacity to absorb DOM than other soil types and high conifer forest coverage that generated acidic litterfall in more sandy watersheds. In contrast, streams with more neutral pH in watersheds with shallow soils had DOM resembling low oxidized phenolic molecules mainly due to increased brush/alder and deciduous vegetation coverage in relatively steeper watersheds. However, as precipitation and flows increased in the fall, the overall water chemistry of streams became more similar as runoff pH increased, the overall chemical diversity of DOM in streams decreased, and stream DOM resembled fresher, lower molecular weight lignin material likely originating from freshly produced leaf litter. Together, our findings show that during hydrologically disconnected periods, pH and landscape characteristics have important controls on the mobilization of aromatic DOM but that many landscape-specific characteristics in the Canadian boreal forest are less influential on DOM processing during wetter conditions where chemically similar, plant-derived DOM signatures are preferentially mobilized. These findings collectively help predict the composition of DOM across diverse watersheds in the Canadian boreal to inform microbial and contaminant biogeochemical processes in downstream ecosystems.

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.

Carbon Budget and Molecular Structure of Natural Organic Matter in Bank Infiltrated Groundwater

Managed aquifer recharge (MAR) provides means to remove natural organic matter (NOM) from surface waters. Recent studies have explored the degree of NOM removal in groundwater. In this study, we further elaborate the NOM removal at a lakeside natural bank infiltration site that functions as a surrogate for MAR. Our objective was to quantify the carbon budget in the aquifer based on concentration measurements of dissolved (in)organic carbon, and the molecular changes in NOM using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). According to the carbon budget, only 25% of the dissolved carbon entering the aquifer was organic, and it predominantly originated from lake water. Of the inorganic majority, on average 40% was produced in the vadose zone above the groundwater table, 31% in the lake bank, 22% in the aquifer as a result of degrading organic matter of lake water, and 7% in the lake. Seasonal concentration variations suggested that the lake bank was the main carbon source in the summer, increasing the carbon concentration of infiltrating lake water, that is, 3.0 mg/L to 7.9 mg/L. FT-ICR MS results showed 4960 to 5330 individual compounds in lake and groundwater. NOM removal in the aquifer was selective: the relative abundance of oxygen-containing species decreased from 75 to 31%, while the relative abundance of sulfur-containing species increased from 15 to 57%. The average molecular weights of both species remained unchanged. The study highlighted the role of lake bank processes and sulfur-containing species in groundwater quality.

Cutting and Bonding Parafilm® to Fast Prototyping Flexible Hanging Drop Chips for 3D Spheroid Cultures

A fast and low-cost fabrication process of flexible hanging drop chips for 3D spheroid cultures was proposed by cutting and bonding Parafilm®, a cohesive thermoplastic. The Parafilm® Hanging Drop Chip (PHDC) was assembled by two-layer of Parafilm® sheet with different sizes of holes. The hole on the upper layer of the Parafilm® is smaller than the hole on the bottom layer. The impact of hole size and sample volume on hanging drop formation and 3D spheroid formations in the hanging drop were investigated. The results showed that 20 µL solution on PHDC with a 3 mm hole could form stabile drop and facilitate spheroid formation. The initial cell number determinates the size of the formed spheroids. Exchanging liquid from the upper hole of the PHDC enables the co-culture of two types of cells in one spheroid and drug efficacy testing in hanging drops. The relative expression of cell adhesion and hypoxia-related genes from spheroids in hanging drop and conventional culture plate suggested the relevance of 3D spheroids and in vivo tumor tissue. The economical hanging drop chip can be fabricated without wet chemistry or expensive fabrication equipment, strengthening its application potential in conventional biological laboratories.

Photoactive Titanium Dioxide Films with Embedded Gold Nanoparticles for Quantitative Determination of Mercury Traces in Humic Matter-Containing Freshwaters

Mercury detection in humic matter-containing natural waters is often associated with environmental harmful substances for sample preparation. Herein we report an approach based on photoactive titanium dioxide films with embedded gold nanoparticles (AuNP@TiO₂ dipstick) for chemical-free sample preparation and mercury preconcentration. For this purpose, AuNPs are immobilized onto a silicon wafer and further covered with a thin photoactive titanium dioxide layer. The AuNPs allow the preconcentration of Hg traces via amalgamation, while TiO₂ acts as a protective layer and, at the same time, as a photocatalyst for UV-C radiation-based sample pretreatment. Humic matter, often present in natural waters, forms stabile complexes with Hg and so hinders its preconcentration prior to detection, causing a minor recovery. This problem is solved here by irradiation during Hg preconcentration onto the photoactive dipstick, resulting in a limit of detection as low as 0.137 ng L^-1 using atomic fluorescence spectrometry (AFS). A 5 min preconcentration step is sufficient to obtain successful recovery of Hg traces from waters with up to 10 mg L^-1 DOC. The feasibility of the approach was demonstrated by the determination of Hg traces in Danube river water. The results show no significant differences in comparison with standard cold vapor-atomic fluorescence spectrometry (CV-AFS) measurements of the same sample. Hence, this new AuNP@TiO₂ dipstick provides a single-step sample preparation and preconcentration approach that combines sustainability with high analytical sensitivity and accuracy.

Simultaneous attenuation of trace organics and change in organic matter composition in the hyporheic zone of urban streams

Trace organic compounds (TrOCs) enter rivers with discharge of treated wastewater. These effluents can contain high loads of dissolved organic matter (DOM). In a 48 h field study, we investigated changes in molecular composition of seven DOM compound classes (FTICR-MS) and attenuation of 17 polar TrOCs in a small urban stream receiving treated wastewater. Correlations between TrOCs and DOM were used to identify simultaneous changes in surface water and the hyporheic zone. Changes in TrOC concentrations in surface water ranged between a decrease of 29.2% for methylbenzotriazole and an increase of 152.2% for the transformation product gabapentin-lactam. In the hyporheic zone, only decreasing TrOC concentrations were observed, ranging from 4.9% for primidone to 93.8% for venlafaxine . TrOC attenuation coincided with a decline of molecular diversity of easily biodegradable DOM compound classes while molecular diversity of poorly biodegradable DOM compound classes increased. This concurrence indicates similar or linked attenuation pathways for biodegradable DOM and TrOCs. Strong correlations between TrOCs and DOM compound classes as well as high attenuation of TrOCs primarily occurred in the hyporheic zone. This suggests high potential for DOM turnover and TrOC mitigation in rivers if hyporheic exchange is sufficient.

Fast Spectrophotometric Method as Alternative for CuO Oxidation to Assess Lignin in Soils with Different Tree Cover

Given the ongoing climate change, estimating the amount of less degradable plant compounds that can be stored in the soil, such as lignin, is a topic of primary importance. There are few methods applicable to soils for the determination of lignin, such as the copper oxide (CuO) oxidation method (CuOL). Acetyl bromide spectrophotometric lignin (ABSL) could be a valid alternative providing information that is less detailed compared to CuOL, but it offers data on the bulk amount of lignin and may offer a valid, fast, and cheap alternative to the CuO method. The aim of this work was to compare ABSL with the CuO method on several soils receiving plant residues from different trees. Mineral soil samples from 0 to 10 cm depth were obtained from a former agricultural site in northern Italy (Brusciana, Tuscany), where different tree plantations were established 22 years ago. The plantations were white poplar and common walnut, which were also intercropped with other species such as hazelnut, Italian alder, and autumn olive. Soil samples under these plantations were also compared to soil under an adjacent agricultural field. In general, the amount of lignin in the afforested stands was approximately double than in the agricultural field as determined by either method. The two methods returned a largely different scale of values due to their different mechanisms of action. The acid-to-aldehyde ratio of syringyl structural units highlights that forest plantation provides a plant input material that is more slowly oxidatively degraded compared to arable soil. A linear mixed model proved that ABSL performed well in relation to CuOL, especially when considering the random variation in the model given by the plantation field design. In conclusion, ABSL can be considered a valid proxy of soil C pool derived from structural plant component, although further analyses are needed.

Molecular differences between water column and sediment pore water SPE-DOM in ten Swedish boreal lakes

Boreal lakes are considered hot spots of dissolved organic matter (DOM) processing within the global carbon cycle. This study has used FT-ICR mass spectrometry and comprehensive data evaluation to assess the molecular differences of SPE-DOM between lake column water SPE-DOM and sedimentary pore water SPE-DOM in 10 Swedish boreal lakes of the Malingsbo area, which were selected for their large diversity of physicochemical and morphological characteristics. While lake column water is well mixed and fairly oxygenated, sedimentary pore water is subject to depletion of oxygen and to confinement of molecules. Robust trends were deduced from molecular compositions present in all compartments and in all 10 lakes ("common compositions") with recognition of relative abundance. Sedimentary pore water SPE-DOM featured higher proportions of heteroatoms N and S, higher average H/C ratios in presence of higher DBE/C ratios, and higher average oxygenation than lake column water SPE-DOM. These trends were observed in all lakes except Ljustjärn, which is a ground water fed kettle lake with an unique lake biogeochemistry. Analogous trends were also observed in case of single or a few lakes and operated also for compounds present solely in either lake column water or sedimentary pore water. Unique compounds detected in either compartments and/or in a few lakes showed higher molecular diversity than the "common compositions". Processing of DOM molecules in sediments included selective preservation for polyphenolic compounds and microbial resynthesis of selected molecules of considerable diversity.

UltraMassExplorer: a browser-based application for the evaluation of high-resolution mass spectrometric data

RATIONALE

High-resolution mass spectrometry (HRMS) with high sample throughput has become an important analytical tool for the analysis of highly complex samples and data processing has become a major challenge for the user community. Evaluating direct-infusion HRMS data without automated tools for batch processing can be a time-consuming step in the analytical pipeline. Therefore, we developed a new browser-based software tool for processing HRMS data.

METHODS

The software, named UltraMassExplorer (UME), was written in the R programming language using the shiny library to build the graphical user interface. The performance of the integrated formula library search algorithm was tested using HRMS data derived from analyses of up to 50 extracts of marine dissolved organic matter.

RESULTS

The software supports the processing of lists of calibrated masses of neutral, protonated or deprotonated molecules, with masses of up to 700 Da and a mass accuracy <3 ppm. In the performance test, the number of assigned peaks per second increased with the number of submitted peaks and reached a maximum rate of 4745 assigned peaks per second.

CONCLUSIONS

UME offers a complete data evaluation pipeline comprising a fast molecular formula assignment algorithm allowing for the swift reanalysis of complete datasets, advanced filter functions and the export of data, metadata and publication-quality graphics. Unique to UME is a fast and interactive connection between data and their visual representation. UME provides a new platform enabling an increased transparency, customization, documentation and comparability of datasets.

The Contribution of Coniferous Canopy to the Molecular Diversity of Dissolved Organic Matter in Rainfall

Rainwater interacts with tree canopies in forest ecosystems, which greatly influence its quality. However, little information is available regarding how tree canopies influence dissolved organic matter (DOM) in rainwater. To examine this, we collected bulk deposition (rainfall) and throughfall in a conifer (Chamaecyparis obtusa) plantation, western Japan, during a rain event, and analyzed their DOM molecular compositions using ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry. The dissolved organic carbon flux and the number of DOM molecular species detected were approximately seven times and three times higher in throughfall than in rainfall, respectively. We found that the average proportion of molecular species shared between five sample replicates was larger in throughfall (69%) than in rainfall (50%). Nonmetric multidimensional scaling revealed that the molecular species were significantly differentiated between throughfall and rainfall, and the dissimilarity among the replicates was much smaller in throughfall. This indicates that the quality of DOM in rainwater became spatially homogeneous due to contact with tree canopies. The number of lignin-like molecules was larger than those of any other biomolecular compounds in throughfall and seven times larger than in rainfall, suggesting that many of plant-derived DOM molecules were dissolved into rainwater.

Extensive processing of sediment pore water dissolved organic matter during anoxic incubation as observed by high-field mass spectrometry (FTICR-MS)

Dissolved organic matter (DOM) contained in lake sediments is a carbon source for many microbial degradation processes, including aerobic and anaerobic mineralization. During anaerobic degradation, DOM is partially consumed and transformed into new molecules while the greenhouse gases methane (CH₄) and carbon dioxide (CO₂) are produced. In this study, we used ultrahigh resolution mass spectrometry to trace differences in the composition of solid-phase extractable (PPL resin) pore water DOM (SPE-DOM) isolated from surface sediments of three boreal lakes before and after 40 days of anoxic incubation, with concomitant determination of CH₄ and CO₂ evolution. CH₄ and CO₂ production detected by gas chromatography varied considerably among replicates and accounted for fractions of ∼2-4 × 10^-4 of sedimentary organic carbon for CO₂ and ∼0.8-2.4 × 10^-5 for CH₄. In contrast, the relative changes of key bulk parameters during incubation, such as relative proportions of molecular series, elemental ratios, average mass and unsaturation, were regularly in the percent range (1-3% for compounds decreasing and 4-10% for compounds increasing), i.e. several orders of magnitude higher than mineralization alone. Computation of the average carbon oxidation state in CHO molecules of lake pore water DOM revealed rather non-selective large scale transformations of organic matter during incubation, with depletion of highly oxidized and highly reduced CHO molecules, and formation of rather non-labile fulvic acid type molecules. In general, proportions of CHO compounds slightly decreased. Nearly saturated CHO and CHOS lipid-like substances declined during incubation: these rather commonplace molecules were less specific indicators of lake sediment alteration than the particular compounds, such as certain oxygenated aromatics and carboxyl-rich alicyclic acids (CRAM) found more abundant after incubation. There was a remarkable general increase in many CHNO compounds during incubation across all lakes. Differences in DOM transformation between lakes corresponded with lake size and water residence time. While in the small lake Svarttjärn, CRAM increased during incubation, lignin-and tannin-like compounds were enriched in the large lake Bisen, suggesting selective preservation of these rather non-labile aromatic compounds rather than recent synthesis. SPE-DOM after incubation may represent freshly synthesized compounds, leftover bulk DOM which is primarily composed of intrinsically refractory molecules and/or microbial metabolites which were not consumed in our experiments. In spite of a low fraction of the total DOM being mineralized to CO₂ and CH₄, the more pronounced change in molecular DOM composition during the incubation indicates that diagenetic modification of organic matter can be substantial compared to complete mineralization.

Characterisation of the semi-volatile component of Dissolved Organic Matter by Thermal Desorption - Proton Transfer Reaction - Mass Spectrometry

Proton Transfer Reaction – Mass Spectrometry (PTR-MS) is a sensitive, soft ionisation method suitable for qualitative and quantitative analysis of volatile and semi-volatile organic vapours. PTR-MS is used for various environmental applications including monitoring of volatile organic compounds (VOCs) emitted from natural and anthropogenic sources, chemical composition measurements of aerosols, etc. Here we apply thermal desorption PTR-MS for the first time to characterise the chemical composition of dissolved organic matter (DOM). We developed a clean, low-pressure evaporation/sublimation system to remove water from samples and coupled it to a custom-made thermal desorption unit to introduce the samples to the PTR-MS. Using this system, we analysed waters from intact and degraded peat swamp forest of Kalimantan, Indonesian Borneo, and an oil palm plantation and natural forest in Sarawak, Malaysian Borneo. We detected more than 200 organic ions from these samples and principal component analysis allowed clear separation of the different sample origins based on the composition of organic compounds. The method is sensitive, reproducible, and provides a new and comparatively cheap tool for a rapid characterisation of water and soil DOM.

Aerosols as a source of dissolved black carbon to the ocean

Dissolved black carbon (DBC) is the largest known slow-cycling organic carbon pool in the world's oceans. Atmospheric deposition could significantly contribute to the oceanic DBC pool, but respective information is lacking. Here we estimate that, during the dust outbreak season, the atmospheric dry deposition of water-soluble black carbon (WSBC) is ~ 40% of the riverine input to the China coastal seas. The molecular composition of atmospheric WSBC determined by ultrahigh-resolution mass spectrometry, reveals similar soil-derived sources as for riverine discharge. WSBC is significantly positively correlated with water-soluble organic carbon (WSOC) in marine aerosols, and water-soluble black carbon contributes on average 2.8 ± 0.65% to the total WSOC. Based on this relationship, the global atmospheric deposition of DBC to the ocean is estimated to be 1.8 ± 0.83 Tg yr^-1. Anticipated future changes in biomass burning and dust mobilization might increase these numbers, with consequences for regional ecosystems and global carbon reservoirs.The contribution of atmospheric deposition to the oceanic dissolved black carbon pool (DBC) is unclear. Here, the authors show that water-soluble black carbon is positively correlated with water-soluble organic carbon in marine aerosols, and that atmospheric deposition is a significant source of oceanic DBC.