The tide-induced resuspension of sediments plays important roles in the efflux of particulate organic carbon (POC) from rivers to the coastal sea. Although dissolved organic carbon (DOC) comprises more than half of the riverine flux of organic carbon to the ocean, the influence of sediment resuspension induced by the tidal cycle on DOC dynamics is largely unknown. This study examined the dynamics of POC, particulate organic nitrogen (PON), DOC, humic-like and protein-like fluorescent dissolved organic matter (DOM) in relation to the tidal cycle in the Chikugo and Hayatsue River Estuaries, Kyushu, Japan. This study is the first to show both the particulate organic matter (POM) and DOM dynamics in relation to the tidal cycle in the macrotidal estuaries. We found that the turbidity changed with the tidal cycle and that there were significant positive correlations of turbidity with POC and PON in the Chikugo River mouth, suggesting that tide-induced sediment resuspension supplied POM to the water column. The DOC concentration, humic-like and protein-like fluorescent DOM were not correlated with turbidity but were negatively correlated with salinity. These results suggest that POM efflux, but not DOM efflux, can be accelerated by tide-induced sediment resuspension in the macrotidal estuaries.

We describe the fate of mangrove leaf tannins in aquatic ecosystems and their possible influence on dissolved organic nitrogen (DON) cycling. Tannins were extracted and purified from senescent yellow leaves of the red mangrove (Rhizophora mangle) and used for a series of model experiments to investigate their physical and chemical reactivity in natural environments. Physical processes investigated included aggregation, adsorption to organic matter‐rich sediments, and co‐aggregation with DON in natural waters. Chemical reactions included structural change, which was determined by excitation‐emission matrix fluorescence spectra, and the release of proteins from tannin‐protein complexes under solar‐simulated light exposure. A large portion of tannins can be physically eliminated from aquatic environments by precipitation in saline water and also by binding to sediments. A portion of DON in natural water can coprecipitate with tannins, indicating that mangrove swamps can influence DON cycling in estuarine environments. The chemical reactivity of tannins in natural waters was also very high, with a half‐life of less than 1 d. Proteins were released gradually from tannin‐protein complexes incubated under light conditions but not under dark conditions, indicating a potentially buffering role of tannin‐ protein complexes on DON recycling in mangrove estuaries. Although tannins are not detected at a significant level in natural waters, they play an important ecological role by preserving nitrogen and buffering its cycling in estuarine ecosystems through the prevention of rapid DON export/loss from mangrove fringe areas and/or from rapid microbial mineralization.

\n Marine dissolved organic nitrogen (DON) is one of the planet’s largest reservoirs of fixed N, which persists even in the N-limited oligotrophic surface ocean. The vast majority of the ocean’s total DON reservoir is refractory (RDON), primarily composed of low molecular weight (LMW) compounds in the subsurface and deep sea. However, the composition of this major N pool, as well as the reasons for its accumulation and persistence, are not understood. Past characterization of the analytically more tractable, but quantitatively minor, high molecular weight (HMW) DON fraction revealed a functionally simple amide-dominated composition. While extensive work in the past two decades has revealed enormous complexity and structural diversity in LMW dissolved organic carbon, no efforts have specifically targeted LMW nitrogenous molecules. Here, we report the first coupled isotopic and solid-state NMR structural analysis of LMW DON isolated throughout the water column in two ocean basins. Together these results provide a first view into the composition, potential sources, and cycling of this dominant portion of marine DON. Our data indicate that RDON is dominated by\n 15\n N-depleted heterocyclic-N structures, entirely distinct from previously characterized HMW material. This fundamentally new view of marine DON composition suggests an important structural control for RDON accumulation and persistence in the ocean. The mechanisms of production, cycling, and removal of these heterocyclic-N-containing compounds now represents a central challenge in our understanding of the ocean’s DON reservoir.\n

Mass spectrometry-based metabolomics approaches can enable detection and quantification of many thousands of metabolite features simultaneously. However, compound identification and reliable quantification are greatly complicated owing to the chemical complexity and dynamic range of the metabolome. Simultaneous quantification of many metabolites within complex mixtures can additionally be complicated by ion suppression, fragmentation and the presence of isomers. Here we present guidelines covering sample preparation, replication and randomization, quantification, recovery and recombination, ion suppression and peak misidentification, as a means to enable high-quality reporting of liquid chromatography- and gas chromatography-mass spectrometry-based metabolomics-derived data.

\n A simple protocol is presented for the solid‐phase extraction of dissolved organic matter (SPE‐DOM) from seawater using commercially prepacked cartridges. The method does not require major instrumentation and can be performed in the field. Modified styrene divinyl benzene polymer type sorbents (Varian PPL and ENV) and sorbents of a silica structure bonded with different hydrocarbon chains (Varian C8, C18, C18OH, and C18EWP) were considered. Except for C18OH, which heavily contaminated the samples, none of the sorbents leached significant amounts of dissolved organic carbon (DOC) or nitrogen (DON). Samples from the North Brazil shelf with strong mixing gradients of terrigenous and marine DOM were used to compare the various sorbents. PPL was the most efficient—on average, 62% of DOC was recovered as salt‐free extracts. C18 was found to be most efficient among the silica‐based sorbents, but it showed only two‐thirds of the extraction efficiency of PPL. As indicated by [\n 1\n H]NMR, C/N, and δ\n 13\n C analyses, PPL extracted a more representative proportion of DOM than C18. Therefore, PPL was used for comparative studies in the Gulf of Mexico and Antarctica. From brackish marsh and river waters, 65% and 62% of total DOC, respectively, could be extracted. For purely marine DOM in Antarctica and the deep sea, the extraction efficiency was lower (43% on average). The efficiency of the new method to isolate marine DOM is better than or similar to highly laborious methods. A further advantage is the complete desalination of the sample. The isolation of a major DOM fraction, which is salt‐free, offers many possibilities to further characterize DOM by advanced analytical techniques.\n

Metabolite profiling in biomarker discovery, enzyme substrate assignment, drug activity/specificity determination, and basic metabolic research requires new data preprocessing approaches to correlate specific metabolites to their biological origin. Here we introduce an LC/MS-based data analysis approach, XCMS, which incorporates novel nonlinear retention time alignment, matched filtration, peak detection, and peak matching. Without using internal standards, the method dynamically identifies hundreds of endogenous metabolites for use as standards, calculating a nonlinear retention time correction profile for each sample. Following retention time correction, the relative metabolite ion intensities are directly compared to identify changes in specific endogenous metabolites, such as potential biomarkers. The software is demonstrated using data sets from a previously reported enzyme knockout study and a large-scale study of plasma samples. XCMS is freely available under an open-source license at http://metlin.scripps.edu/download/.

Liquid chromatography - mass spectrometry (LC-MS) based untargeted metabolomics allows to measure both known and unknown metabolites in the metabolome. However, unknown metabolite annotation is a major challenge in untargeted metabolomics. Here, we develop an approach, namely, knowledge-guided multi-layer network (KGMN), to enable global metabolite annotation from knowns to unknowns in untargeted metabolomics. The KGMN approach integrates three-layer networks, including knowledge-based metabolic reaction network, knowledge-guided MS/MS similarity network, and global peak correlation network. To demonstrate the principle, we apply KGMN in an in vitro enzymatic reaction system and different biological samples, with ~100-300 putative unknowns annotated in each data set. Among them, >80% unknown metabolites are corroborated with in silico MS/MS tools. Finally, we validate 5 metabolites that are absent in common MS/MS libraries through repository mining and synthesis of chemical standards. Together, the KGMN approach enables efficient unknown annotations, and substantially advances the discovery of recurrent unknown metabolites for common biological samples from model organisms, towards deciphering dark matter in untargeted metabolomics.© 2022. The Author(s).

Metabolism has an essential role in biological systems. Identification and quantitation of the compounds in the metabolome is defined as metabolic profiling, and it is applied to define metabolic changes related to genetic differences, environmental influences and disease or drug perturbations. Chromatography-mass spectrometry (MS) platforms are frequently used to provide the sensitive and reproducible detection of hundreds to thousands of metabolites in a single biofluid or tissue sample. Here we describe the experimental workflow for long-term and large-scale metabolomic studies involving thousands of human samples with data acquired for multiple analytical batches over many months and years. Protocols for serum- and plasma-based metabolic profiling applying gas chromatography-MS (GC-MS) and ultraperformance liquid chromatography-MS (UPLC-MS) are described. These include biofluid collection, sample preparation, data acquisition, data pre-processing and quality assurance. Methods for quality control-based robust LOESS signal correction to provide signal correction and integration of data from multiple analytical batches are also described.

Microbes drive ecosystems and their viruses manipulate these processes, yet the importance of tidal functioning on the estuarine viruses and microbes remains poorly elucidated. Here, an integrative investigation on tidal patterns in viral and microbial communities and their inherent interactions over an entire spring-neap tidal cycle was conducted along a macrotidal subtropical estuary. The viral and microbial abundances oscillated significantly over the tidal cycle with relatively higher abundances observed at spring tide compared to neap tide. The distinct tidal dynamic patterns in bacterial production and community composition were tightly associated with the variations in viral infection, production and decay, revealing the tide-driven interactions between viruses and microbes. Concurrent with the higher viral decay but lower bacterial abundance and inhibited bacterial metabolism during the neap tide, lower gross viral production was coupled with a synchronous switching from viral lytic to lysogenic infection induced by the loss of viral infection efficiency and the transition from marine to freshwater bacterial populations triggered by tidal mixing. Our results highlighted the major tidal impact on the microbial dynamics through virus-host interactions, with cascading effects, neglected so far, on estuarine biogeochemical cycles.Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.

Analyzing the molecular composition change of dissolved organic matter (DOM) during transportation in estuaries can enhance our understanding of the fate of DOM. However, the impact of hydrologic conditions resulting from large river plumes on the DOM cycle are less explored, and previous studies were insufficient to capture the molecular fate that occur during the transportation process. In this study, we used a range of bulk and optical techniques, as well as Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), to determine the concentration and characteristics of DOM along two trajectories of downstream plumes of diluted water of the Yangtze (Changjiang) River estuary (YRE) during the high discharge season. These two plumes situated along the route of the summer Changjiang diluted water (CDW) have been identified and named CDW-North (CDW-N) and CDW-South (CDW-S), respectively. Despite having the same riverine end-member origin, the turbidity zone in YRE significantly modifies the molecular characteristics and composition of DOM. The results of FT-ICR MS indicated a spatial variation of DOM composition in the coastal zone of the two plumes. The relative intensities of the CHO, CHOS, and CHONS compounds are negatively correlated with salinity. In addition, the coastal zones of both CDW-N and CDW-S are characterized by more autochthonous DOM sources. More CHON compounds in CDW-N are probably due to the production of autochthonous DOM in offshore waters. The activity of phytoplankton increased the surface dissolved oxygen level of CDW-N in the coastal zone. However, the hypoxic zone formed at the bottom of the CDW-N due to microbial degradation of organic matter and may further benefit the preservation of CHON compounds. Our study emphasizes that the characteristics and composition of the estuarine DOM can be significantly shaped by distinct large river plumes. Furthermore, using FT-ICR MS in combination with complementary techniques can better assist in identifying the sources and transformation mechanisms of estuarine DOM in large river plume-affected systems and provide more valuable insights into the role of DOM in the estuarine biogeochemical cycle.© 2023 The Authors. Published by American Chemical Society.