Data evaluation strategy for identification of key molecular formulas in dissolved organic matter as proxies for biogeochemical reactivity based on abundance differences from ultrahigh resolution mass spectrometry

Thermodynamics and explainable machine learning assist in interpreting biodegradability of dissolved organic matter in sludge anaerobic digestion with thermal hydrolysis

Dissolved organic matter (DOM) is essential in biological treatment, yet its specific roles remain incompletely understood. This study introduces a machine learning (ML) framework to interpret DOM biodegradability in the anaerobic digestion (AD) of sludge, incorporating a thermodynamic indicator (λ). Ensemble models such as Xgboost and LightGBM achieved high accuracy (training: 0.90-0.98; testing: 0.75-0.85). The explainability of the ML models revealed that the features λ, measured m/z, nitrogen to carbon ratio (N/C), hydrogen to carbon ratio (H/C), and nominal oxidation state of carbon (NOSC) were significant formula features determining biodegradability. Shapley values further indicated that the biodegradable DOM were mostly formulas with λ lower than 0.03, measured m/z value higher than 600 Da, and N/C ratios higher than 0.2. This study suggests that a strategy based on ML and its explainability, considering formula features, particularly thermodynamic indicators, provides a novel approach for understanding and estimating the biodegradation of DOM.

The loss of dissolved organic matter from biological soil crust at various successional stages under rainfall of different intensities: Insights into the changes of molecular components at different rainfall stages

Biological soil crusts (BSCs) are typical covers in arid and semiarid regions. The dissolved organic matter (DOM) of BSCs can be transported to various aquatic ecosystems by rainfall-runoff processes. However, the spatiotemporal variation in quality and quantity of DOM in runoff remains unclear. Herein, four kinds of runoff plots covered by four successional stages of BSCs were set up on slopes, including bare runoff plot (BR), cyanobacteria crust covered runoff plot (CR), mixed crust covered runoff plot (MIR), and moss crust covered runoff plot (MOR). The quantity and quality of DOM in runoff during rainfall was investigated based on the stimulated rainfall experiments combined with optical spectroscopy and ultra-high resolution mass spectrometry analyses. The results showed that the DOM concentrations (i.e., 0.30 to 45.25 mg L-1) in runoff followed the pattern of MOR>MIR>CR>BR, and they were exponentially decreased with rainfall duration. The DOM loss rate of BR (8.26 to 11.64 %) was significantly greater than those of CR, MIR, and MOR (0.84 to 3.22 %). Highly unsaturated compounds (HUCs), unsaturated aliphatic compounds (UACs), saturated compounds (SCs), and peptide-like compounds (PLCs) were the dominated compounds of the water extractable DOM from the original soils. Thereinto, PLCs and UACs were more easily leached into runoff during rainfall. The relatively intensity of HUCs in runoff generally decreased with rainfall duration, while the relatively intensities of UACs, PLCs, and SCs slightly increased with rainfall duration. These findings suggested that the DOM loss rate was effectively decreased with the successional of BSCs during rainfall; meanwhile, some labile compounds (e.g., PLCs and UACs) were transported into various aquatic ecosystems by rainfall-runoff processes.

Post column infusion of an internal standard into LC-FT-ICR MS enables semi-quantitative comparison of dissolved organic matter in original samples

Ultrahigh resolution mass spectrometry hyphenated with liquid chromatography (LC) is an emerging tool to explore the isomeric composition of dissolved organic matter (DOM). However, matrix effects limit the potential for semi-quantitative comparison of DOM molecule abundances across samples. We introduce a post-column infused internal standard (PCI-IS) for reversed-phase LC-FT-ICR MS measurements of DOM and systematically evaluate matrix effects, detector linearity and the precision of mass peak intensities. Matrix effects for model compounds spiked into freshwater DOM samples ranging from a headwater stream to a major river were reduced by 5-10% for PCI-IS corrected mass peak intensities as compared to raw (i.e., untransformed) intensities. A linear regression of PCI-IS corrected DOM mass peak intensities across a typical DOM concentration range (2-15 mg dissolved organic carbon L-1) in original, non-extracted freshwater samples demonstrates excellent linearity of the detector response (r2 > 0.9 for 98% of detected molecular formulas across retention times). Importantly, PCI-IS could compensate for 80% of matrix effects across an environmental gradient of DOM composition from groundwater to surface water. This enabled studying the ionization efficiency of DOM isomers and linking the observed differences to the biogeochemical sources. With PCI-IS original, non-extracted DOM samples can be analysed by LC-FT-ICR MS without carbon load adjustment, and mass peak intensities can be reliably used to semi-quantitatively compare isomer abundances between compositionally similar DOM samples.

Chemodiversity of riverine dissolved organic matter: Effects of local environments and watershed characteristics

Riverine dissolved organic matter (DOM) is crucial to global carbon cycling and aquatic ecosystems. However, the geographical patterns and environmental drivers of DOM chemodiversity remain elusive especially in the waters and sediments of continental rivers. Here, we systematically analyzed DOM molecular diversity and composition in surface waters and sediments across 97 broadly distributed rivers using data from the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) consortium. We further examined the associations of molecular richness and composition with geographical, climatic, physicochemical variables, as well as the watershed characteristics. We found that molecular richness significantly decreased toward higher latitudes, but only in sediments (r = -0.24, p < 0.001). The environmental variables like precipitation and non-purgeable organic carbon showed strong associations with DOM molecular richness and composition. Interestingly, we identified that less-documented factors like watershed characteristics were also related to DOM molecular richness and composition. For instance, DOM molecular richness was positively correlated with the soil sand fraction for waters, while with the percentage of forest for sediments. Importantly, the effects of watershed characteristics on DOM molecular richness and composition were generally stronger in waters than sediments. This phenomenon was further supported by the fact that 11 out of 13 watershed characteristics (e.g., the percentages of impervious area and cropland) showed more positive than negative correlations with molecular abundance especially in waters. As the percentage of forest increased, there was a continuous accumulation of the compounds with higher molecular weight, aromaticity, and degree of unsaturation. In contrast, human activities accumulated the compounds with lower molecular weight and oxygenation, and higher bioavailability. Our findings imply that it may be possible to use a small set of broadly available data types to predict DOM molecular richness and composition across diverse river systems. Elucidation of mechanisms underlying these relationships will provide further enhancements to such predictions, especially when extrapolating to unsampled systems.

Characteristics of dissolved organic matter (DOM) in Chinese farmland soils under different climate zone types: A molecular perspective

Interactions between dissolved organic matter (DOM) and surrounding environments are highly complex. Understanding DOM at the molecular level can contribute to the management of soil pollution and safeguarding agricultural fields. Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) has enabled a molecular-level understanding of DOM. Accordingly, in this study, we investigated soil samples from 27 different regions of mainland China with various soil types and climatic characteristics. Based on the geographical features of the four typical climatic zones in mainland China (temperate monsoon, temperate continental, subtropical monsoon, and Qinghai-Tibet Plateau climates), we employed high-resolution mass spectrometry to determine the molecular diversity of DOM under different climatic conditions. The results indicated that lignin and tannin-like substances were the most active categories of DOM in the soils. Collectively, the composition and unsaturation of DOM molecules are influenced by sunlight, precipitation, temperature, and human activity. All climatic regions contained a substantial number of characteristic molecules, with CHO and CHON constituting over 80%, and DOM containing nitrogen and sulfur was relatively more abundant in the monsoon regions. The complex composition of DOM incorporates various active functional groups, such as -NO2 and -ONO2. Furthermore, soil DOM in the monsoon regions showed higher unsaturation and facilitated various (bio) biochemical reactions in the soil.

Dissolved organic matter cycling revealed from the molecular level in three coastal bays of China

As the widespread distributed and critical zones connecting the land and ocean systems, coastal bays are special units with semi-enclosed landforms to accommodate and process dissolved organic matter (DOM) in the context of increasing anthropogenic effects globally. However, compared to other common systems that have been paid much attention to (e.g., large river estuaries, wetlands), the roles of the coastal bays in coastal carbon cycling are less explored. To fill this knowledge gap, here we combined optical techniques and ultra-high-resolution mass spectrometry to systematically investigate the DOM chemistry of the three typical coastal bays in different nutrient levels, Xiangshan Bay, Jiaozhou Bay, and Sishili Bay, in China. Results show that terrestrial signals and anthropogenic imprints were observed in these three bays to various extents. Besides, Xiangshan Bay with a higher nutrient level had the DOM characterized by lower humification and aromaticity degree than Jiaozhou Bay and Sishili Bay, which not likely mainly resulted from the differences in the primary production or photochemical processing. Further examination reveals that microbial processing likely contributes to the differences in DOM chemistry among the three bays, as indicated by different proportions of potentially transformed nitrogen-containing molecules and relative abundances of the island of stability molecules. Considering the nutrient levels in different bays, we speculate that the lower nutrient concentrations would promote the efficiency of the microbial carbon pump (MCP), which hypothesized that heterotrophic microorganisms might contribute to the formation of marine recalcitrant organic carbon. Additionally, the enrichment of oxygen-rich compounds in the unique carboxyl-rich alicyclic molecule pool of Jiaozhou Bay and Sishili Bay suggests that the efficient MCP might preferentially form them in these two bays. This study emphasizes the importance of coordinating the land and ocean systems and controlling the nutrient discharge to coastal bays, thus, to potentially promote long-term marine carbon sequestration.

Water-soluble organic carbon (WSOC) from vegetation fire and its differences from WSOC in natural media: Spectral comparison and self-organizing maps (SOM) classification

Vegetation fire frequently occurs globally and produces two types of water-soluble organic carbon (WSOC) including black carbon WSOC (BC-WSOC) and smoke-WSOC, they will eventually enter the surface environment (soil and water) and participate in the eco-environmental processes on the earth surface. Exploring the unique features of BC-WSOC and smoke-WSOC is critical and fundamental for understanding their eco-environmental effects. Presently, their differences from the natural WSOC of soil and water remain unknown. This study produced various BC-WSOC and smoke-WSOC by simulating vegetation fire and used UV-vis, fluorescent EEM-PARAFAC, and fluorescent EEM-SOM to analyze their different features from natural WSOC of soil and water. The results showed that the maximum yield of smoke-WSOC reached about 6600 folds that of BC-WSOC after a vegetation fire event. The increasing burning temperature decreased the yield, molecular weight, polarity, and protein-like matters abundance of BC-WSOC and increased the aromaticity of BC-WSOC, but presented a negligible effect on the features of smoke-WSOC. Furthermore, compared with natural WSOC, BC-WSOC had a greater aromaticity, smaller molecular weight, and more humic-like matters, while smoke-WSOC had a lower aromaticity, smaller molecular size, higher polarity, and more protein-like matters. EEM-SOM analysis indicated that the ratio between the fluorescence intensity at Ex/Em: 275 nm/320 nm and the sum fluorescence intensity at Ex/Em: 275 nm/412 nm and Ex/Em: 310 nm/420 nm could effectively differentiate WSOC of different sources, following the order of smoke-WSOC (0.64-11.38) > water-WSOC and soil-WSOC (0.06-0.76) > BC-WSOC (0.0016-0.04). Hence, BC-WSOC and smoke-WSOC possibly directly alter the quantity, properties, and organic compositions of WSOC in soil and water. Owing to smoke-WSOC having far greater yield and bigger difference from natural WSOC than BC-WSOC, the eco-environmental effect of smoke-WSOC deposition should be given more attention after a vegetation fire.

Unraveling the photochemical reactivity of dissolved organic matter in the Yangtze river estuary: Integrating incubations with field observations

Dissolved organic matter (DOM) sustains a substantial part of the organic matter transported seaward in large estuaries, where photochemical reactions significantly influence its transformation and fate. Irradiation experiments can provide valuable information on the photochemical reactivity (photo-labile, photo-resistant, and photo-product) of molecules. However, previous research paid less attention to exploring the controls of the initial DOM chemistry to irradiation experiments and examining the applicability of their further integration with field research. Here, we conducted irradiation experiments for samples from the freshwater and seawater endmember of the Yangtze River Estuary (YRE), which receives organic matter transport from the largest river in China, the Yangtze River. Molecules that occurred before and after irradiation experiments were characterized by the Fourier transform ion cyclotron resonance mass spectrometry. Results show that both post-irradiation samples have the lower aromaticity degree and reduced oxidation state, while the freshwater endmember sample exhibits more dramatic changes, indicating the controls of parent molecules to the effect of irradiation experiments. Integrating with the "molecular matching" approach, we compared the molecules occurring in field samples with the classified molecules (photo-resistant, photo-labile, and photo-product) acquired from performed irradiation experiments and correlated the relative intensity of photochemical reactivity types with salinity. When applying results from different experiments to conduct "molecular matching", the photo-resistant and photo-labile relative intensity possess consistently positive and negative trends with increasing salinity, respectively. This suggests their reliability for molecular matching applications, while the inconsistent trends for the photo-product relative intensity with salinity suggest its uncertainty in assessing the photo-induced effects. Moreover, the molecular composition within the photochemical reactivity types in field samples also evolved along the salinity gradient and showed similar trends with the DOM changes after experimental irradiation. Despite various factors influencing estimations, it is revealed that a fraction of aromatic molecules and majority of carboxyl-rich alicyclic molecules considered with biologically persistent nature in the YRE freshwater zone are simultaneously not susceptible to photochemical transformation to potentially constitute a long-term marine carbon sink. This study emphasizes the importance and limitations of the combination of field research and laboratory-controlled experiments to provide a better understanding of the crucial role of photochemical reactions in affecting carbon cycling in large estuaries.

Niche differentiation of microbial community shapes vertical distribution of recalcitrant dissolved organic matter in deep-sea sediments

Sedimentary organic matter provides carbon substrates and energy sources for microorganisms, which drive benthic biogeochemical processes and in turn modify the quantity and quality of dissolved organic matter (DOM). However, the molecular composition and distribution of DOM and its interactions with microbes in deep-sea sediments remain poorly understood. Here, molecular composition of DOM and its relationship with microbes were analyzed in samples collected from two sediment cores (∼40 cm below the sea floor), at depths of 1157 and 2253 m from the South China Sea. Results show that niche differentiation was observed on a fine scale in different sediment layers, with Proteobacteria and Nitrososphaeria dominating the shallow sediments (0-6 cm) and Chloroflexi and Bathyarchaeia prevailing in deeper sediments (6-40 cm), indicating correspondence of microbial community composition with both geographical isolation and the availability of organic matter. An intimate link between the DOM composition and microbial community further indicates that, microbial mineralization of fresh organic matter in the shallow layer potentially resulted in the accumulation of recalcitrant DOM (RDOM), while relatively low abundance of RDOM was linked to anaerobic microbial utilization in deeper sediment layers. In addition, higher RDOM abundance in the overlying water, as compared to that in the surface sediment, suggests that sediment might be a source of deep-sea RDOM. These results emphasize the close relation between the distribution of sediment DOM and different microbial community, laying a foundation for understanding the complex dynamics of RDOM in deep-sea sediment and water column.