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Organic matter (OM) is central to biogeochemical processes in both soils and aquatic systems. Water-soluble organic matter (WSOM), leached from soil, is widely analyzed as a proxy for the mobile OM fraction, yet the chemical composition of extracts depends strongly on the extraction method used. We compared two WSOM extraction protocols—distilled water and 0.5 M K 2 SO 4 —across 217 soil samples from 83 depth profiles spanning four central European regions. Absorbance and fluorescence spectroscopy with PARAFAC modeling were used to characterize dissolved organic carbon (DOC) concentration and composition—approaches increasingly applied in soil science to trace soil organic matter dynamics. DOC generally declined with profile depth. K 2 SO 4 extracts consistently yielded higher DOC concentrations, dominated by humic-like fluorescence. Water extracts were more variable, with stronger protein-like signals—showing clearer depth-related trends, with deeper layers enriched in microbially-derived DOM. This higher variability likely reflects the dynamic nature of labile WSOM fractions. We highlight the importance of extraction chemistry: water-based methods capture reactive, microbially-produced WSOM—likely indicators of immediate inputs to aquatic systems, whereas salt-based methods emphasize more stable pools—acting as indicators of less bio-available, long-term terrestrial reservoirs. Extraction methodology selection should consider the study objectives and specific biological and physicochemical processes investigated.

Headwater streams influence the biogeochemical characteristics of large rivers and play important roles in regional and global carbon budgets. The combined effects of seasonality and land use change on the biogeochemistry of headwater streams, however, are not well understood. In this study we assessed the influence of catchment land use and seasonality on the composition of dissolved organic matter (DOM) and ecosystem metabolism in headwater streams of a Kenyan river. Fifty sites in 34 streams draining a gradient of catchment land use from 100% natural forest to 100% agriculture were sampled to determine temporal and spatial variation in DOM composition. Gross primary production (GPP) and ecosystem respiration (ER) were determined in 10 streams draining primarily forest or agricultural catchments. Absorbance and fluorescence spectrophotometry of DOM reflected notable shifts in composition along the land use gradient and with season. During the dry season, forest streams contained higher molecular weight and terrestrially derived DOM, whereas agricultural streams were dominated by autochthonous production and low molecular weight DOM. During the rainy season, aromaticity and high molecular weight DOM increased in agricultural streams, coinciding with seasonal erosion of soils and inputs of organic matter from farmlands. Most of the streams were heterotrophic. However, GPP and ER were generally greater in agricultural streams, driven by higher dissolved nutrient (mainly TDN) concentrations, light availability (open canopy) and temperature compared with forest streams. There were correlations between freshly and autochthonously produced DOM, GPP and ER during both the dry and wet seasons. This is one of the few studies to link land-use with organic carbon dynamics and DOM composition. Measures of ecosystem metabolism in these streams help to affirm the role of tropical streams and rivers as important components of the global carbon cycle and demonstrate that even semi-intensive, smallholder agriculture can have measurable effects on riverine ecosystem functioning.

Aim: The need to go beyond taxonomy to understand patterns in microbial function has led to an increased use of trait-based approaches, yet we know little about how microbial functional traits vary across large-scale environmental gradients in natural ecosystems. Here, we apply a trait-based approach to explore the large-scale variability in the trait structure underlying the processing of dissolved organic matter (DOM) by boreal bacterioplankton communities, as well as its regulation and links to taxonomic composition. Location: Samples were collected from 296 rivers and lakes across five regions in northern Quebec (Canada), which span large gradients in environmental, climatic and geographical properties typical of the boreal zone. Methods: We used the metabolic profiles obtained with Biolog EcoPlates® as an imprint of the trait structure underlying bacterial processing of DOM, and Illumina sequencing of the 16SrRNA gene to characterize the taxonomic composition of these bacterial assemblages. The resulting spatial patterns were compared with an array of climatic, landscape and limnological properties varying at the landscape scale. Results: Despite a clear regional segregation of the sampled sites based on environmental variables, the trait structure of boreal bacteria did not show any regional or ecosystem-specific patterns, but rather was linked to a gradient of quality of DOM. Community trait configurations diverged progressively with decreasing terrestrial influence, probably due to local processes that transform and diversify the available pool of DOM. This DOM quality gradient did not explain the taxonomic biogeography of these communities, which was controlled by a different set of environmental factors. Main conclusions: The functional biogeography of boreal bacterioplankton is driven by the nature of the DOM pool, and particularly by the influence of terrestrial DOM. The lack of coherence between functional and taxonomic biogeographies implies that the environmental controls of freshwater bacterial performance cannot be directly inferred from spatial patterns in taxonomic composition.

Graphical AbstractDiagram illustrating site-specific and depth-specific dissolved organic matter (DOM) composition changes. It features four soil types: Peat, Peaty Gleysol, Podzol, and Cambisol, each with processes like anaerobic preservation and microbial processing. Depth-specific changes are shown with arrows, indicating how shared compounds' abundance alters with depth. The right side shows surface water flow.

The nitrogen contamination in rivers has become significant concern in arid and semiarid areas due to water resource shortage and extensive anthropogenic activities in relation to land-use changes in China. As a major nitrogen species, identifying driving factors, transformation and sources of nitrate is crucial for managing nitrogen pollution in rivers. In this study, nitrate sources and transformations were deciphered using physicochemical variables, molecular signature of dissolved organic matter and coupled isotopes of nitrate under different land use types in the Yang River, a typical farming-pastoral ecotone in the semi-arid area of North China. The results of river water showed a significant positive correlation between NO 3 − concentrations, δ 15 N-NO 3 − values and percentage of urban land and cropland, which confirmed the critical role of land use in the variations of riverine nitrate. The correlation between dissolved organic matter composition (aliphatic and lignin-like compounds) and NO 3 − /Cl − ratios as well as Cl − concentrations verified the effect of agricultural activities on nitrate source and transport. The variation in water chemical variables and dual isotopes of nitrate in river and soil extracts (δ 15 N-NO 3 − and δ 18 O-NO 3 − ) was indicative of the concurrence of in-soil nitrification process and assimilation, whereas denitrification was inhibited under aerobic conditions in the semiarid area. The Bayesian model revealed that about 60% of nitrate was derived from non-point sources (manure, soil organic nitrogen and chemical fertilizer) and 36% from sewage. Although urban is not the major land-use type in the farming-pastoral ecotone, sewage contributed to about 36% of nitrate. The source identification of nitrate stresses the importance of the management of non-point pollution and demand for sewage treatment facilities in the farming-pastoral ecotone. This multiple-tracer approach will help gain deeper insights into nitrogen management in semi-arid areas with extensive human disturbance.

Dinitrogen (N₂) fixation by diazotrophs supports ocean productivity. Diazotrophs include photoautotrophic cyanobacteria, non-cyanobacterial diazotrophs (NCDs), and the recently discovered N2-fixing haptophyte. While NCDs are ubiquitous in the ocean, their ecology and metabolism remain largely unknown. Unlike cyanobacterial diazotrophs and the haptophyte, NCDs are primarily heterotrophic and depend on dissolved organic matter (DOM) for carbon and energy. However, conventional DOM amendment incubations do not allow discerning how different diazotrophs use DOM molecules, limiting our knowledge on DOM–diazotroph interactions. To identify diazotrophs using DOM, we amended North Pacific microbial communities with 13C-labeled DOM from phytoplankton cultures that was molecularly characterized, revealing the dominance of nitrogen-rich compounds. After DOM additions, we observed a community shift from cyanobacterial diazotrophs like Crocosphaera and Trichodesmium to NCDs at stations where the N2-fixing haptophyte abundance was relatively low. Through DNA stable isotope probing and gene sequencing, we identified diverse diazotrophs capable of taking up DOM. Our findings highlight unexpected DOM uptake by the haptophyte’s nitroplast, changes in community structure, and previously unrecognized osmotrophic behavior in NCDs, shaped by local biogeochemical conditions.

Dissolved organic matter (DOM) is a key component in the carbon and energy cycling of soil and aquatic ecosystems. Tracking DOM composition through soil profiles provides insight into the processes driving its transport and transformation. However, there is a lack of studies investigating whether DOM composition in deeper mineral soil is driven by topsoil inputs, or if processes during soil passage cause a rather uniform DOM quality irrespective of the source. Understanding the topsoil influence on subsoil DOM and depth-dependent transformation patterns is crucial for the transfer to and its fate within aquatic ecosystems. To address this knowledge gap, we examined the compositional features of DOM sampled in situ along depth profiles of four contrasting soil types (Peat, peaty Gleysol, Cambisol, Podzol) in a mountainous catchment (Ore Mountains, Germany). A combination of pyrolysis-gas chromatography/mass spectrometry and UV and fluorescence spectroscopy was used to characterize the molecular properties of DOM and similarities across the different soils and depths were achieved by Bray-Curtis dissimilarity analysis. Results revealed site-specific decreases in similarity with depth, driven by soil processes that progressively alter DOM composition. In Peat, composition remained rather similar between D1 and D2 or D3 (57-59%), likely due to constantly anoxic conditions that inhibit oxidative degradation and transformation of DOM. In the peaty Gleysol, moderate transformations were observed (41-59% similarity), likely driven by alternating redox conditions and sorptive interactions. The strongest compositional changes occurred in the Cambisol with similarity between D1 and D3 reaching 18%, suggesting microbial processing in conjunction with sorptive interactions with the mineral phase. In the Podzol, the formation of organo-metal complexes promoted selective preservation of aromatic structures. The site-specific processes led to decreases in both the number and abundance of identified shared compounds with depth, contrasting the assumption of DOM similarity across different soil types. Despite the changes with depth, subsoil DOM composition in Peat, peaty Gleysol, and Podzol still retained some imprint of topsoil sources. This study highlights how site-specific biotic and abiotic processing generates unique DOM composition that shape organic matter cycling in soils and its ecological implications in aquatic systems.

Extreme events such as hurricanes and tropical storms often result in large fluxes of dissolved organic carbon (DOC) to estuaries. Precipitation associated with tropical storms may be increasing in the southeastern U.S., which can potentially impact dissolved organic matter (DOM) dynamics and cycling in coastal systems. Here, DOM composition at the Altamaha River and Estuary (Georgia, U.S.A.) was investigated over multiple years capturing seasonal variations in river discharge, high precipitation events, and the passage of two hurricanes which resulted in substantial storm surges. Optical measurements of DOM indicate that the terrigenous signature in the estuary is linearly related to freshwater content and is similar after extreme events with or without a storm surge and during peak river flow. Molecular level analysis revealed significant differences, however, with a large increase of highly aromatic compounds after extreme events exceeding what would be expected by freshwater content alone. Although extreme events are often followed by increased DOC biodegradation, the terrigenous material added during those events does not appear to be more labile than the remainder of the DOM pool that was captured by ultrahigh-resolution mass spectrometry analysis. This suggests that the added terrigenous organic matter may be exported to the coastal ocean, while a fraction of the organic matter that co-varied with the terrigenous DOM may contribute to the increased biomineralization in the estuary, with implications to carbon processing in coastal areas.

Dissolved organic matter (DOM) is a key soil quality property, indicative of the organic matter stored in the soil, which may also be a function of temporal variation. This study examines whether DOM is a robust property of the soil, controlling fertility, or if it may change with time. Altogether eight sets of soil samples were collected in 2018 and 2019 from the cultivated topsoil (0–10 cm) of cropland and from a nearby grassland near Martonvásár, Hungary. The study sites were characterized by Chernozem soil and were part of a long-term experimental project comparing the effects of manure application and fertilization to the control under maize and wheat monocultures. DOM was extracted from the samples with distilled water. The dissolved organic carbon (DOC), total dissolved nitrogen (DN), biological index (BIX), fluorescence index (FI), humification index (HIX), carbon nitrogen (C/N) ratio and specific ultraviolet absorbance at 254 nm (SUVA254) index were studied in the arable soils, and the results showed that all the DOM samples were humified, suggesting relevant microbiological contributions to the decomposition of OM and its conversion into more complex molecules (FI = 1.2–1.5, BIX = ~0.5, and HIX = ~0.9). Temporal variations were detected only for the permanent grassland where higher DOM concentration was found in spring. This increased DOM content mainly originated from humified, solid phase associated, recalcitrant OM. In contrast, there were no differences among fertilization treatments and sampling dates under cropfield conditions. Moreover, climatic conditions were not proven as a general ruler of DOM properties. Therefore, momentary DOM alone is not necessarily the direct property of soil organic matter under cropfield conditions. The application of this measure needs further details of sampling conditions to achieve adequate comparability.

Microbially-mediated transformations of dissolved organic matter (DOM) in a marsh-dominated estuarine system were investigated at the molecular level using ultrahigh resolution mass spectrometry. In addition to observing spatial and temporal variability in DOM sources in the estuary, multiple incubations with endogenous microorganisms identified the influence of DOM composition on biodegradation. A clear microbial preference for degradation of compounds associated with marine DOM relative to those of terrestrial origin was observed, resulting in an overall shift of the remaining DOM toward a stronger terrigenous signature. During short, one-day long incubations of samples rich in marine DOM, the molecular formulae that were enriched had slightly smaller mass (20-30 Da) and number of carbon atoms compared to the molecular formulae that were depleted. Over longer time scales (70 days), the mean differences in molecular mass between formulae that were depleted and enriched were substantially larger (~270 Da). The differences in elemental composition over daily time scales were consistent with transformations in functional groups; over longer time scales, the differences in elemental composition may be related to progressive transformations of functional groups of intermediate products and/or other reactions. Our results infused new data toward the understanding of DOM processing by bacterioplankton in estuarine systems.